RNA Interference Mediated Inhibition of MAP Kinase Gene Expression or Expression of Genes Involved in MAP Kinase Pathway Using Short Interfering Nucleic Acid (SiNA)

ABSTRACT

The present invention concerns methods and reagents useful in modulating MAP kinase gene expression in a variety of applications, including use in therapeutic, diagnostic, target validation, and genomic discovery applications. Specifically, the invention relates to small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules capable of mediating RNA interference (RNAi) against c-JUN, JNK, p38, and ERK gene expression, useful in the treatment of cancer, inflammation, obesity and insulin resistance (e.g. Type I and Type II diabetes).

This application is a continuation of U.S. patent application Ser. No. 10/424,339, filed Apr. 25, 2003, which is a continuation-in-part of International Patent Application No. PCT/US03/02510, filed Jan. 28, 2003, and is a continuation-in-part of International Patent Application No. PCT/US03/05346, filed Feb. 20, 2003, and is a continuation-in-part of International Patent Application No. PCT/US03/05028, filed Feb. 20, 2003, which each claim the benefit of U.S. Provisional Application No. 60/358,580 filed Feb. 20, 2002, U.S. Provisional Application No. 60/363,124 filed Mar. 11, 2002, U.S. Provisional Application No. 60/386,782 filed Jun. 6, 2002, U.S. Provisional Application No. 60/406,784 filed Aug. 29, 2002, U.S. Provisional Application No. 60/408,378 filed Sep. 5, 2002, U.S. Provisional Application No. 60/409,293 filed Sep. 9, 2002, and U.S. Provisional Application No. 60/440,129 filed Jan. 15, 2003. The instant application claims the benefit of all the listed applications, which are hereby incorporated by reference herein in their entireties, including the drawings.

SEQUENCE LISTING

The sequence listing submitted via EFS, in compliance with 37 CFR § 1.52(e)(5), is incorporated herein by reference. The sequence listing text file submitted via EFS contains the file “SequenceListing45USCNT”, created on Aug. 27, 2008, which is 468,031 bytes in size.

FIELD OF THE INVENTION

The present invention concerns compounds, compositions, and methods for the study, diagnosis, and treatment of conditions and diseases that respond to the modulation of mitogen activated protein kinase (MAP kinase) gene expression and/or activity. The present invention also concerns compounds, compositions, methods relating to the modulation of expression or activity of genes involved in the MAP kinase pathway. Specifically, the invention relates to small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules capable of mediating RNA interference (RNAi) against genes involved in the Jun amino-terminal kinase (JNK), p38, and/or ERK pathway, such as c-JUN. More specifically, the invention relates to small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules capable of mediating RNA interference (RNAi) against Jun amino-terminal kinase (JNK), p38, ERK, and/or c-JUN genes.

BACKGROUND OF THE INVENTION

The following is a discussion of relevant art pertaining to RNAi. The discussion is provided only for understanding of the invention that follows. The summary is not an admission that any of the work described below is prior art to the claimed invention.

RNA interference refers to the process of sequence-specific post-transcriptional gene silencing in animals mediated by short interfering RNAs (siRNAs) (Fire et al., 1998, Nature, 391, 806). The corresponding process in plants is commonly referred to as post-transcriptional gene silencing or RNA silencing and is also referred to as quelling in fungi. The process of post-transcriptional gene silencing is thought to be an evolutionarily-conserved cellular defense mechanism used to prevent the expression of foreign genes and is commonly shared by diverse flora and phyla (Fire et al., 1999, Trends Genet., 15, 358). Such protection from foreign gene expression may have evolved in response to the production of double-stranded RNAs (dsRNAs) derived from viral infection or from the random integration of transposon elements into a host genome via a cellular response that specifically destroys homologous single-stranded RNA or viral genomic RNA. The presence of dsRNA in cells triggers the RNAi response though a mechanism that has yet to be fully characterized. This mechanism appears to be different from the interferon response that results from dsRNA-mediated activation of protein kinase PKR and 2′,5′-oligoadenylate synthetase resulting in non-specific cleavage of mRNA by ribonuclease L.

The presence of long dsRNAs in cells stimulates the activity of a ribonuclease III enzyme referred to as dicer. Dicer is involved in the processing of the dsRNA into short pieces of dsRNA known as short interfering RNAs (siRNAs) (Berstein et al., 2001, Nature, 409, 363). Short interfering RNAs derived from dicer activity are typically about 21 to about 23 nucleotides in length and comprise about 19 base pair duplexes (Elbashir et al., 2001, Genes Dev., 15, 188). Dicer has also been implicated in the excision of 21- and 22-nucleotide small temporal RNAs (stRNAs) from precursor RNA of conserved structure that are implicated in translational control (Hutvagner et al., 2001, Science, 293, 834). The RNAi response also features an endonuclease complex, commonly referred to as an RNA-induced silencing complex (RISC), which mediates cleavage of single-stranded RNA having sequence complementary to the antisense strand of the siRNA duplex. Cleavage of the target RNA takes place in the middle of the region complementary to the antisense strand of the siRNA duplex (Elbashir et al., 2001, Genes Dev., 15, 188).

RNAi has been studied in a variety of systems. Fire et al., 1998, Nature, 391, 806, were the first to observe RNAi in C. elegans. Wianny and Goetz, 1999, Nature Cell Biol., 2, 70, describe RNAi mediated by dsRNA in mouse embryos. Hammond et al., 2000, Nature, 404, 293, describe RNAi in Drosophila cells transfected with dsRNA. Elbashir et al., 2001, Nature, 411, 494, describe RNAi induced by introduction of duplexes of synthetic 21-nucleotide RNAs in cultured mammalian cells including human embryonic kidney and HeLa cells. Recent work in Drosophila embryonic lysates (Elbashir et al., 2001, EMBO J., 20, 6877) has revealed certain requirements for siRNA length, structure, chemical composition, and sequence that are essential to mediate efficient RNAi activity. These studies have shown that 21-nucleotide siRNA duplexes are most active when containing 3′-terminal dinucleotide overhangs. Furthermore, complete substitution of one or both siRNA strands with 2′-deoxy (2′-H) or 2′-O-methyl nucleotides abolishes RNAi activity, whereas substitution of the 3′-terminal siRNA overhang nucleotides with 2′-deoxy nucleotides (2′-H) was shown to be tolerated. Single mismatch sequences in the center of the siRNA duplex were also shown to abolish RNAi activity. In addition, these studies also indicate that the position of the cleavage site in the target RNA is defined by the 5′-end of the siRNA guide sequence rather than the 3′-end of the guide sequence (Elbashir et al., 2001, EMBO J., 20, 6877). Other studies have indicated that a 5′-phosphate on the target-complementary strand of a siRNA duplex is required for siRNA activity and that ATP is utilized to maintain the 5′-phosphate moiety on the siRNA (Nykanen et al., 2001, Cell, 107, 309).

Studies have shown that replacing the 3′-terminal nucleotide overhanging segments of a 21-mer siRNA duplex having two-nucleotide 3′-overhangs with deoxyribonucleotides does not have an adverse effect on RNAi activity. Replacing up to four nucleotides on each end of the siRNA with deoxyribonucleotides has been reported to be well tolerated, whereas complete substitution with deoxyribonucleotides results in no RNAi activity (Elbashir et al., 2001, EMBO J., 20, 6877). In addition, Elbashir et al., supra, also report that substitution of siRNA with 2′-O-methyl nucleotides completely abolishes RNAi activity. Li et al., International PCT Publication No. WO 00/44914, and Beach et al., International PCT Publication No. WO 01/68836 preliminarily suggest that siRNA may include modifications to either the phosphate-sugar backbone or the nucleoside to include at least one of a nitrogen or sulfur heteroatom, however, neither application postulates to what extent such modifications would be tolerated in siRNA molecules, nor provides any further guidance or examples of such modified siRNA. Kreutzer et al., Canadian Patent Application No. 2,359,180, also describe certain chemical modifications for use in dsRNA constructs in order to counteract activation of double-stranded RNA-dependent protein kinase PKR, specifically 2′-amino or 2′-methyl nucleotides, and nucleotides containing a 2′-O or 4′-C methylene bridge. However, Kreutzer et al. similarly fails to provide examples or guidance as to what extent these modifications would be tolerated in siRNA molecules.

Parrish et al., 2000, Molecular Cell, 6, 1977-1087, tested certain chemical modifications targeting the unc-22 gene in C. elegans using long (>25 nt) siRNA transcripts. The authors describe the introduction of thiophosphate residues into these siRNA transcripts by incorporating thiophosphate nucleotide analogs with T7 and T3 RNA polymerase and observed that RNAs with two phosphorothioate modified bases also had substantial decreases in effectiveness as RNAi. Further, Parrish et al. reported that phosphorothioate modification of more than two residues greatly destabilized the RNAs in vitro such that interference activities could not be assayed. Id. at 1081. The authors also tested certain modifications at the 2′-position of the nucleotide sugar in the long siRNA transcripts and found that substituting deoxynucleotides for ribonucleotides produced a substantial decrease in interference activity, especially in the case of Uridine to Thymidine and/or Cytidine to deoxy-Cytidine substitutions. Id. In addition, the authors tested certain base modifications, including substituting, in sense and antisense strands of the siRNA, 4-thiouracil, 5-bromouracil, 5-iodouracil, and 3-(aminoallyl)uracil for uracil, and inosine for guanosine. Whereas 4-thiouracil and 5-bromouracil substitution appeared to be tolerated, Parrish reported that inosine produced a substantial decrease in interference activity when incorporated in either strand. Parrish also reported that incorporation of 5-iodouracil and 3-(aminoallyl)uracil in the antisense strand resulted in a substantial decrease in RNAi activity as well.

The use of longer dsRNA has been described. For example, Beach et al., International PCT Publication No. WO 01/68836, describes specific methods for attenuating gene expression using endogenously-derived dsRNA. Tuschl et al., International PCT Publication No. WO 01/75164, describe a Drosophila in vitro RNAi system and the use of specific siRNA molecules for certain functional genomic and certain therapeutic applications; although Tuschl, 2001, Chem. Biochem., 2, 239-245, doubts that RNAi can be used to cure genetic diseases or viral infection due to the danger of activating interferon response. Li et al., International PCT Publication No. WO 00/44914, describe the use of specific dsRNAs for attenuating the expression of certain target genes. Zernicka-Goetz et al., International PCT Publication No. WO 01/36646, describe certain methods for inhibiting the expression of particular genes in mammalian cells using certain dsRNA molecules. Fire et al., International PCT Publication No. WO 99/32619, describe particular methods for introducing certain dsRNA molecules into cells for use in inhibiting gene expression. Plaetinck et al., International PCT Publication No. WO 00/01846, describe certain methods for identifying specific genes responsible for conferring a particular phenotype in a cell using specific dsRNA molecules. Mello et al., International PCT Publication No. WO 01/29058, describe the identification of specific genes involved in dsRNA-mediated RNAi. Deschamps Depaillette et al., International PCT Publication No. WO 99/07409, describe specific compositions consisting of particular dsRNA molecules combined with certain anti-viral agents. Waterhouse et al., International PCT Publication No. 99/53050, describe certain methods for decreasing the phenotypic expression of a nucleic acid in plant cells using certain dsRNAs. Driscoll et al., International PCT Publication No. WO 01/49844, describe specific DNA constructs for use in facilitating gene silencing in targeted organisms.

Others have reported on various RNAi and gene-silencing systems. For example, Parrish et al., 2000, Molecular Cell, 6, 1977-1087, describe specific chemically-modified siRNA constructs targeting the unc-22 gene of C. elegans. Grossniklaus, International PCT Publication No. WO 01/38551, describes certain methods for regulating polycomb gene expression in plants using certain dsRNAs. Churikov et al., International PCT Publication No. WO 01/42443, describe certain methods for modifying genetic characteristics of an organism using certain dsRNAs. Cogoni et al., International PCT Publication No. WO 01/53475, describe certain methods for isolating a Neurospora silencing gene and uses thereof. Reed et al., International PCT Publication No. WO 01/68836, describe certain methods for gene silencing in plants. Honer et al., International PCT Publication No. WO 01/70944, describe certain methods of drug screening using transgenic nematodes as Parkinson's Disease models using certain dsRNAs. Deak et al., International PCT Publication No. WO 01/72774, describe certain Drosophila-derived gene products that may be related to RNAi in Drosophila. Arndt et al., International PCT Publication No. WO 01/92513 describe certain methods for mediating gene suppression by using factors that enhance RNAi. Tuschl et al., International PCT Publication No. WO 02/44321, describe certain synthetic siRNA constructs. Pachuk et al., International PCT Publication No. WO 00/63364, and Satishchandran et al., International PCT Publication No. WO 01/04313, describe certain methods and compositions for inhibiting the function of certain polynucleotide sequences using certain dsRNAs. Echeverri et al., International PCT Publication No. WO 02/38805, describe certain C. elegans genes identified via RNAi. Kreutzer et al., International PCT Publications Nos. WO 02/055692, WO 02/055693, and EP 1144623 B1 describes certain methods for inhibiting gene expression using RNAi. Graham et al., International PCT Publications Nos. WO 99/49029 and WO 01/70949, and AU 4037501 describe certain vector expressed siRNA molecules. Fire et al., U.S. Pat. No. 6,506,559, describe certain methods for inhibiting gene expression in vitro using certain long dsRNA (greater than 25 nucleotide) constructs that mediate RNAi.

SUMMARY OF THE INVENTION

This invention relates to compounds, compositions, and methods useful for modulating the expression of genes associated with mitogen activated protein kinase (MAP kinase) gene expression pathways (see for example FIG. 12) by RNA interference (RNAi) using short interfering nucleic acid (siNA) molecules. In particular, the instant invention features small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules and methods used to modulate the expression of MAP kinase genes, including c-JUN, JNK genes such as JNK1 and JNK2, ERK genes such as ERK1 and ERK2, and p38 genes. A siNA of the invention can be unmodified or chemically-modified. A siNA of the instant invention can be chemically synthesized, expressed from a vector or enzymatically synthesized. The instant invention also features various chemically-modified synthetic short interfering nucleic acid (siNA) molecules capable of modulating telomerase gene expression or activity in cells by RNA interference (RNAi). The use of chemically-modified siNA improves various properties of native siNA molecules through increased resistance to nuclease degradation in vivo and/or through improved cellular uptake. Further, contrary to earlier published studies, siNA having multiple chemical modifications retains its RNAi activity. The siNA molecules of the instant invention provide useful reagents and methods for a variety of therapeutic, diagnostic, target validation, genomic discovery, genetic engineering, and pharmacogenomic applications.

In one embodiment, the invention features one or more siNA molecules and methods that independently or in combination modulate the expression of gene(s) encoding MAP kinase proteins, such as genes encoding sequences comprising those sequences referred to by GenBank Accession Nos. shown in Table I, referred to herein generally as MAP kinases. The description below of the various aspects and embodiments of the invention is provided with reference to exemplary MAP kinases such as JNK1 (also referred to as MAPK8, for example Genbank Accession No. NM_(—)002750), p38 (also referred to as MAPK14, for example Genbank Accession No. NM_(—)139012), ERK2 (also referred to as MAPK1, for example Genbank Accession No. NM_(—)002745), and ERK1 (also referred to as MAPK3, for example Genbank Accession XM_(—)055766) genes. However, the various aspects and embodiments are also directed to other MAP kinases referred to by Accession number in Table 1 and other genes involved in MAP kinase pathways such those genes encoding c-JUN (for example Genbank Accession No. NM_(—)002228), TNF-alpha (for example Genbank Accession No. M10988), interleukins such as IL-8 (for example Genbank Accession No. M68932), and activating proteins such as AP-1 (for example Genbank Accession No. NM_(—)013277). The various aspects and embodiments are also directed to other genes that are involved in the MAP kinase pathways of gene expression. Those additional genes can be analyzed for target sites using the methods described for MAP kinase genes herein. Thus, the inhibition and the effects of such inhibition of the other genes can be performed as described herein.

In one embodiment, the invention features a siNA molecule that down-regulates expression of a MAP kinase gene, for example, wherein the MAP kinase gene comprises MAP kinase encoding sequence (e.g., c-JUN, JNK1, JNK2, p38, ERK1, or ERK2).

In one embodiment, the invention features a siNA molecule having RNAi activity against MAP kinase RNA, wherein the siNA molecule comprises a sequence complementary to an RNA having MAP kinase encoding sequence, such as those sequences having MAP kinase GenBank Accession Nos. shown in Table I. In another embodiment, the invention features a siNA molecule having RNAi activity against MAP kinase RNA, wherein the siNA molecule comprises a sequence complementary to an RNA having other MAP kinase encoding sequence, such as mutant MAP kinase genes, splice variants of MAP kinase genes, and other MAP kinase ligands and receptors. Chemical modifications as shown in Tables III and IV or otherwise described herein can be applied to any siNA construct of the invention.

In another embodiment, the invention features a siNA molecule having RNAi activity against a MAP kinase gene, wherein the siNA molecule comprises nucleotide sequence complementary to nucleotide sequence of a MAP kinase gene, such as those MAP kinase sequences having GenBank Accession Nos. shown in Table I or other MAP kinase encoding sequence, such as mutant MAP kinase genes, splice variants of MAP kinase genes, and other MAP kinase ligands and receptors. In another embodiment, a siNA molecule of the invention includes nucleotide sequence that can interact with nucleotide sequence of a MAP kinase gene and thereby mediate silencing of MAP kinase gene expression, for example, wherein the siNA mediates regulation of MAP kinase gene expression by cellular processes that modulate the chromatin structure of the MAP kinase gene and prevent transcription of the MAP kinase gene.

In another embodiment, the invention features a siNA molecule comprising nucleotide sequence, for example, nucleotide sequence in the antisense region of the siNA molecule, that is complementary to a nucleotide sequence or portion of sequence of a MAP kinase gene. In another embodiment, the invention features a siNA molecule comprising a region, for example, the antisense region of the siNA construct, complementary to a sequence comprising a MAP kinase gene sequence or a portion thereof.

In one embodiment, the antisense region of ERK2 siNA constructs can comprise a sequence complementary to sequence having any of SEQ ID NOs. 1-163, or 1113-1116. The antisense region can also comprise sequence having any of SEQ ID NOs. 164-326, 1133-1136, 1141-1144, or 1149-1152. In another embodiment, the sense region of ERK2 siNA constructs can comprise sequence having any of SEQ ID NOs. 1-163, 1113-1116, 1129-1132, 1137-1140, or 1145-1148.

In one embodiment, the antisense region of ERK1 siNA constructs can comprise a sequence complementary to sequence having any of SEQ ID NOs. 327-431, or 1117-1120. The antisense region can also comprise sequence having any of SEQ ID NOs. 432-536, 1157-1160, 1165-1168, or 1173-1176. In another embodiment, the sense region of ERK1 siNA constructs can comprise sequence having any of SEQ ID NOs. 327-431, 1117-1120, 1153-1156, 1161-1164, or 1169-1172.

In one embodiment, the antisense region of JNK1 siNA constructs can comprise a sequence complementary to sequence having any of SEQ ID NOs. 537-615 or 1121-1124. The antisense region can also comprise sequence having any of SEQ ID NOs. 616-694, 1181-1184, 1189-1192, 1197-1200, 1237, 1239, 1241, 1243, 1245, or 1246. In another embodiment, the sense region of JNK1 constructs can comprise sequence having any of SEQ ID NOs. 537-615, 1121-1124, 1177-1180, 1185-1188, 1193-1196, 1236, 1238, 1240, 1242, or 1244. The sense region can comprise a sequence of SEQ ID NO. 1225 and the antisense region can comprise a sequence of SEQ ID NO. 1226. The sense region can comprise a sequence of SEQ ID NO. 1227 and the antisense region can comprise a sequence of SEQ ID NO. 1228. The sense region can comprise a sequence of SEQ ID NO. 1229 and the antisense region can comprise a sequence of SEQ ID NO. 1230. The sense region can comprise a sequence of SEQ ID NO. 1231 and the antisense region can comprise a sequence of SEQ ID NO. 1232. The sense region can comprise a sequence of SEQ ID NO. 1233 and the antisense region can comprise a sequence of SEQ ID NO. 1234. The sense region can comprise a sequence of SEQ ID NO. 1231 and the antisense region can comprise a sequence of SEQ ID NO. 1235.

In one embodiment, the antisense region of p38 siNA constructs can comprise a sequence complementary to sequence having any of SEQ ID NOs. 695-903 or 1125-1128. The antisense region can also comprise sequence having any of SEQ ID NOs. 904-1112, 1205-1208, 1213-1216, or 1221-1224. In another embodiment, the sense region of p38 siNA constructs can comprise sequence having any of SEQ ID NOs. 695-903, 1125-1128, 1201-1204, 1209-1212, or 1217-1220.

In one embodiment, the antisense region of c-JUN siNA constructs can comprise a sequence complementary to sequence having any of SEQ ID NOs. 1247-1427 or 1609-1616. In one embodiment, the antisense region of c-JUN siNA constructs can comprise sequence having any of SEQ ID NOs. 1428-1608, 1625-1632, 1641-1648, 1657-1664, 1673-1680, 1698, 1700, 1702, 1705, 1707, 1709, 1711, or 1714. In another embodiment, the sense region of c-JUN siNA constructs can comprise sequence having any of SEQ ID NOs. 1247-1427, 1609-1616, 1617-1624, 1633-1640, 1649-1656, 1665-1672, 1697, 1699, 1701, 1703, 1704, 1706, 1708, 1710, 1712, or 1713.

In one embodiment, a siNA molecule of the invention comprises any of SEQ ID NOs. 1-1714. The sequences shown in SEQ ID NOs: 1-1714 are not limiting. A siNA molecule of the invention can comprise any contiguous MAP kinase sequence (e.g., about 19 to about 25, or about 19, 20, 21, 22, 23, 24 or 25 contiguous MAP kinase nucleotides).

In yet another embodiment, the invention features a siNA molecule comprising a sequence, for example, the antisense sequence of the siNA construct, complementary to a sequence or portion of sequence comprising sequence represented by GenBank Accession Nos. shown in Table I. Chemical modifications in Tables III and IV and described herein can be applied to any siRNA construct of the invention.

In one embodiment of the invention a siNA molecule comprises an antisense strand having about 19 to about 29 nucleotides, wherein the antisense strand is complementary to a RNA sequence encoding a MAP kinase protein, and wherein said siNA further comprises a sense strand having about 19 to about 29 (e.g., about 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29) nucleotides, and wherein said sense strand and said antisense strand are distinct nucleotide sequences with at least about 19 complementary nucleotides.

In another embodiment of the invention a siNA molecule of the invention comprises an antisense region having about 19 to about 29 (e.g., about 19, 20, 21, 22, 23, 24, 25, 26, 27, 28 or 29) nucleotides, wherein the antisense region is complementary to a RNA sequence encoding a MAP kinase protein, and wherein said siNA further comprises a sense region having about 19 to about 29 nucleotides, wherein said sense region and said antisense region comprise a linear molecule with at least about 19 complementary nucleotides.

In one embodiment of the invention a siNA molecule comprises an antisense strand comprising a nucleotide sequence that is complementary to a nucleotide sequence encoding a MAP kinase protein or a portion thereof. The siNA further comprises a sense strand, wherein said sense strand comprises a nucleotide sequence of a MAP kinase gene or a portion thereof.

In another embodiment, a siNA molecule comprises an antisense region comprising a nucleotide sequence that is complementary to a nucleotide sequence encoding a MAP kinase protein or a portion thereof. The siNA molecule further comprises a sense region, wherein said sense region comprises a nucleotide sequence of a MAP kinase gene or a portion thereof.

In one embodiment, a siNA molecule of the invention has RNAi activity that modulates expression of RNA encoded by a MAP kinase gene. Because MAP kinase genes can share some degree of sequence homology with each other, siNA molecules can be designed to target a class of MAP kinase genes (and associated receptor or ligand genes) or alternately specific MAP kinase genes by selecting sequences that are either shared amongst different MAP kinase targets or alternatively that are unique for a specific MAP kinase target. Therefore, in one embodiment, the siNA molecule can be designed to target conserved regions of MAP kinase RNA sequence having homology between several MAP kinase genes so as to target several MAP kinase genes (e.g., different MAP kinase isoforms, splice variants, mutant genes etc.) with one siNA molecule. In another embodiment, the siNA molecule can be designed to target a sequence that is unique to a specific MAP kinase RNA sequence due to the high degree of specificity that the siNA molecule requires to mediate RNAi activity.

In one embodiment, nucleic acid molecules of the invention that act as mediators of the RNA interference gene silencing response are double-stranded nucleic acid molecules. In another embodiment, the siNA molecules of the invention consist of duplexes containing about 19 base pairs between oligonucleotides comprising about 19 to about 25 (e.g., about 19, 20, 21, 22, 23, 24 or 25) nucleotides. In yet another embodiment, siNA molecules of the invention comprise duplexes with overhanging ends of about 1 to about 3 (e.g., about 1, 2, or 3) nucleotides, for example, about 21-nucleotide duplexes with about 19 base pairs and 3′-terminal mononucleotide, dinucleotide, or trinucleotide overhangs.

In one embodiment, the invention features one or more chemically-modified siNA constructs having specificity for MAP kinase expressing nucleic acid molecules, such as RNA encoding a MAP kinase protein. Non-limiting examples of such chemical modifications include without limitation phosphorothioate internucleotide linkages, 2′-deoxyribonucleotides, 2′-O-methyl ribonucleotides, 2′-deoxy-2′-fluoro ribonucleotides, “universal base” nucleotides, “acyclic” nucleotides, 5-C-methyl nucleotides, and terminal glyceryl and/or inverted deoxy abasic residue incorporation. These chemical modifications, when used in various siNA constructs, are shown to preserve RNAi activity in cells while at the same time, dramatically increasing the serum stability of these compounds. Furthermore, contrary to the data published by Parrish et al., supra, applicant demonstrates that multiple (greater than one) phosphorothioate substitutions are well-tolerated and confer substantial increases in serum stability for modified siNA constructs.

In one embodiment, a siNA molecule of the invention comprises modified nucleotides while maintaining the ability to mediate RNAi. The modified nucleotides can be used to improve in vitro or in vivo characteristics such as stability, activity, and/or bioavailability. For example, a siNA molecule of the invention can comprise modified nucleotides as a percentage of the total number of nucleotides present in the siNA molecule. As such, a siNA molecule of the invention can generally comprise about 5% to about 100% modified nucleotides (e.g., 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% modified nucleotides). The actual percentage of modified nucleotides present in a given siNA molecule will depend on the total number of nucleotides present in the siNA. If the siNA molecule is single stranded, the percent modification can be based upon the total number of nucleotides present in the single stranded siNA molecules. Likewise, if the siNA molecule is double stranded, the percent modification can be based upon the total number of nucleotides present in the sense strand, antisense strand, or both the sense and antisense strands.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a MAP kinase gene, wherein the siNA molecule comprises one or more chemical modifications and each strand of the double-stranded siNA is about 21 nucleotides long.

In one embodiment, a siNA molecule of the invention does not contain any ribonucleotides. In another embodiment, a siNA molecule of the invention comprises one or more ribonucleotides.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a MAP kinase gene, wherein one of the strands of the double-stranded siNA molecule comprises a nucleotide sequence that is complementary to a nucleotide sequence of the MAP kinase gene or a portion thereof, and wherein the second strand of the double-stranded siNA molecule comprises a nucleotide sequence substantially similar to the nucleotide sequence of the MAP kinase gene or a portion thereof.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a MAP kinase gene, wherein each strand of the siNA molecule comprises about 19 to about 23 nucleotides, and wherein each strand comprises at least about 19 nucleotides that are complementary to the nucleotides of the other strand.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a MAP kinase gene, wherein the siNA molecule comprises an antisense region comprising a nucleotide sequence that is complementary to a nucleotide sequence of the MAP kinase gene or a portion thereof, and wherein the siNA further comprises a sense region, wherein the sense region comprises a nucleotide sequence substantially similar to the nucleotide sequence of the MAP kinase gene or a portion thereof.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a MAP kinase gene, wherein the antisense region and the sense region each comprise about 19 to about 23 nucleotides, and wherein the antisense region comprises at least about 19 nucleotides that are complementary to nucleotides of the sense region.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a MAP kinase gene, wherein the siNA molecule comprises a sense region and an antisense region and wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of RNA encoded by the MAP kinase gene or a portion thereof and the sense region comprises a nucleotide sequence that is complementary to the antisense region.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a MAP kinase gene, wherein the siNA molecule is assembled from two separate oligonucleotide fragments wherein one fragment comprises the sense region and the second fragment comprises the antisense region of the siNA molecule. The sense region can be connected to the antisense region via a linker molecule, such as a polynucleotide linker or a non-nucleotide linker.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a MAP kinase gene, wherein the siNA molecule comprises a sense region and an antisense region and wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of RNA encoded by the MAP kinase gene or a portion thereof and the sense region comprises a nucleotide sequence that is complementary to the antisense region, wherein the siNA molecule has one or more modified pyrimidine and/or purine nucleotides. In one embodiment, the pyrimidine nucleotides in the sense region are 2′-O-methylpyrimidine nucleotides, or 2′-deoxy-2′-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2′-deoxy purine nucleotides. In another embodiment, the pyrimidine nucleotides in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2′-O-methyl purine nucleotides. In another embodiment of any of the above described siNA molecules, any nucleotides present in a non-complementary region of the sense strand (e.g. overhang region) are 2′-deoxy nucleotides.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a MAP kinase gene, wherein the siNA molecule is assembled from two separate oligonucleotide fragments wherein one fragment comprises the sense region and the second fragment comprises the antisense region of the siNA molecule, and wherein the fragment comprising the sense region includes a terminal cap moiety at the 5′-end, the 3′-end, or both of the 5′ and 3′ ends of the fragment comprising the sense region. In one embodiment, the terminal cap moiety is an inverted deoxy abasic moiety or glyceryl moiety. In one embodiment, each of the two fragments of the siNA molecule comprises about 21 nucleotides.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a MAP kinase gene, wherein the siNA molecule comprises a sense region and an antisense region and wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence or a portion thereof of RNA encoded by the MAP kinase gene and the sense region comprises a nucleotide sequence that is complementary to the antisense region, and wherein the purine nucleotides present in the antisense region comprise 2′-deoxy-purine nucleotides. In another embodiment, the purine nucleotides present in the antisense region comprise 2′-O-methyl purine nucleotides. In either of the above embodiments, the antisense region comprises a phosphorothioate internucleotide linkage at the 3′ end of the antisense region. In an alternative embodiment, the antisense region comprises a glyceryl modification at the 3′ end of the antisense region. In another embodiment of any of the above described siNA molecules, any nucleotides present in a non-complementary region of the antisense strand (e.g. overhang region) are 2′-deoxy nucleotides.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a MAP kinase gene, wherein the siNA molecule is assembled from two separate oligonucleotide fragments each comprising 21 nucleotides, wherein one fragment comprises the sense region and the second fragment comprises the antisense region of the siNA molecule, and wherein about 19 nucleotides of each fragment of the siNA molecule are base-paired to the complementary nucleotides of the other fragment of the siNA molecule and wherein at least two 3′ terminal nucleotides of each fragment of the siNA molecule are not base-paired to the nucleotides of the other fragment of the siNA molecule. In one embodiment, each of the two 3′ terminal nucleotides of each fragment of the siNA molecule is a 2′-deoxy-pyrimidine, such as 2′-deoxy-thymidine. In another embodiment, all 21 nucleotides of each fragment of the siNA molecule are base-paired to the complementary nucleotides of the other fragment of the siNA molecule. In another embodiment, about 19 nucleotides of the antisense region are base-paired to the nucleotide sequence or a portion thereof of the RNA encoded by the MAP kinase gene. In another embodiment, 21 nucleotides of the antisense region are base-paired to the nucleotide sequence or a portion thereof of the RNA encoded by the MAP kinase gene. In any of the above embodiments, the 5′-end of the fragment comprising said antisense region can optionally include a phosphate group.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits the expression of a MAP kinase RNA sequence (e.g., wherein said target RNA sequence is encoded by a MAP kinase gene or a gene involved in the MAP kinase pathway), wherein the siNA molecule does not contain any ribonucleotides and wherein each strand of the double-stranded siNA molecule is about 21 nucleotides long.

In one embodiment, the invention features a medicament comprising a siNA molecule of the invention.

In one embodiment, the invention features an active ingredient comprising a siNA molecule of the invention.

In one embodiment, the invention features the use of a double-stranded short interfering nucleic acid (siNA) molecule to down-regulate expression of a MAP kinase gene, wherein the siNA molecule comprises one or more chemical modifications and each strand of the double-stranded siNA is about 21 nucleotides long.

The invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a MAP kinase gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of a MAP kinase RNA or a portion thereof, the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification. In one embodiment, the nucleotide sequence of the antisense strand of the double-stranded siNA molecule is complementary to the nucleotide sequence of the MAP kinase RNA which encodes a protein or a portion thereof. In one embodiment, each strand of the siNA molecule comprises about 19 to about 29 nucleotides, and each strand comprises at least about 19 nucleotides that are complementary to the nucleotides of the other strand. In one embodiment, the siNA molecule is assembled from two oligonucleotide fragments, wherein one fragment comprises the nucleotide sequence of the antisense strand of the siNA molecule and a second fragment comprises nucleotide sequence of the sense region of the siNA molecule. In another embodiment, the sense strand is connected to the antisense strand via a linker molecule, such as a polynucleotide linker or a non-nucleotide linker. In one embodiment, the pyrimidine nucleotides present in the sense strand are 2′-deoxy-2′-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2′-deoxy purine nucleotides. In another embodiment, the pyrimidine nucleotides present in the sense strand are 2′-deoxy-2′-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2′-O-methyl purine nucleotides. In one embodiment, wherein the sense strand comprises a 3′-end and a 5′-end, a terminal cap moiety (e.g., an inverted deoxy abasic moiety) is present at the 5′-end, the 3′-end, or both of the 5′ and 3′ ends of the sense strand. In one embodiment, the antisense strand comprises one or more 2′-deoxy-2′-fluoro pyrimidine nucleotides and one or more 2′-O-methyl purine nucleotides. In one embodiment, the pyrimidine nucleotides present in the antisense strand are 2′-deoxy-2′-fluoro pyrimidine nucleotides and any purine nucleotides present in the antisense strand are 2′-O-methyl purine nucleotides. In one embodiment, the antisense strand comprises a phosphorothioate internucleotide linkage at the 3′ end of the antisense strand. In another embodiment, the antisense strand comprises a glyceryl modification at the 3′ end. In another embodiment, the 5′-end of the antisense strand optionally includes a phosphate group. In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a MAP kinase gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of MAP kinase RNA or a portion thereof, the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification, and wherein the nucleotide sequence of the antisense strand is complementary to a nucleotide sequence of the 5′-untranslated region or a portion thereof of the MAP kinase RNA. In another embodiment, the nucleotide sequence of the antisense strand is complementary to a nucleotide sequence of the MAP kinase RNA or a portion thereof.

In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a MAP kinase gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of MAP kinase RNA or a portion thereof, the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification, and wherein each of the two strands of the siNA molecule comprises 21 nucleotides. In one embodiment, about 19 nucleotides of each strand of the siNA molecule are base-paired to the complementary nucleotides of the other strand of the siNA molecule and at least two 3′ terminal nucleotides of each strand of the siNA molecule are not base-paired to the nucleotides of the other strand of the siNA molecule. In one embodiment, each of the two 3′ terminal nucleotides of each fragment of the siNA molecule are 2′-deoxy-pyrimidines, such as 2′-deoxy-thymidine. In another embodiment, each strand of the siNA molecule is base-paired to the complementary nucleotides of the other strand of the siNA molecule. In one embodiment, about 19 nucleotides of the antisense strand are base-paired to the nucleotide sequence of the MAP kinase RNA or a portion thereof. In another embodiment, 21 nucleotides of the antisense strand are base-paired to the nucleotide sequence of the MAP kinase RNA or a portion thereof.

In one embodiment, the invention features a composition comprising a siNA molecule of the invention and a pharmaceutically acceptable carrier or diluent.

In one embodiment, the invention features the use of a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a MAP kinase gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of MAP kinase RNA or a portion thereof, the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification.

In a non-limiting example, the introduction of chemically-modified nucleotides into nucleic acid molecules provides a powerful tool in overcoming potential limitations of in vivo stability and bioavailability inherent to native RNA molecules that are delivered exogenously. For example, the use of chemically-modified nucleic acid molecules can enable a lower dose of a particular nucleic acid molecule for a given therapeutic effect since chemically-modified nucleic acid molecules tend to have a longer half-life in serum. Furthermore, certain chemical modifications can improve the bioavailability of nucleic acid molecules by targeting particular cells or tissues and/or improving cellular uptake of the nucleic acid molecule. Therefore, even if the activity of a chemically-modified nucleic acid molecule is reduced as compared to a native nucleic acid molecule, for example, when compared to an all-RNA nucleic acid molecule, the overall activity of the modified nucleic acid molecule can be greater than that of the native molecule due to improved stability and/or delivery of the molecule. Unlike native unmodified siNA, chemically-modified siNA can also minimize the possibility of activating interferon activity in humans.

In any of the embodiments of siNA molecules described herein, the antisense region of a siNA molecule of the invention can comprise a phosphorothioate internucleotide linkage at the 3′-end of said antisense region. In any of the embodiments of siNA molecules described herein, the antisense region can comprise about one to about five phosphorothioate internucleotide linkages at the 5′-end of said antisense region. In any of the embodiments of siNA molecules described herein, the 3′-terminal nucleotide overhangs of a siNA molecule of the invention can comprise ribonucleotides or deoxyribonucleotides that are chemically-modified at a nucleic acid sugar, base, or backbone. In any of the embodiments of siNA molecules described herein, the 3′-terminal nucleotide overhangs can comprise one or more universal base ribonucleotides. In any of the embodiments of siNA molecules described herein, the 3′-terminal nucleotide overhangs can comprise one or more acyclic nucleotides.

One embodiment of the invention provides an expression vector comprising a nucleic acid sequence encoding at least one siNA molecule of the invention in a manner that allows expression of the nucleic acid molecule. Another embodiment of the invention provides a mammalian cell comprising such an expression vector. The mammalian cell can be a human cell. The siNA molecule of the expression vector can comprise a sense region and an antisense region. The antisense region can comprise sequence complementary to an RNA or DNA sequence encoding MAP kinase and the sense region can comprise sequence complementary to the antisense region. The siNA molecule can comprise two distinct strands having complementary sense and antisense regions. The siNA molecule can comprise a single strand having complementary sense and antisense regions.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against a MAP kinase inside a cell or reconstituted in vitro system, wherein the chemical modification comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) nucleotides comprising a backbone modified internucleotide linkage having Formula I:

wherein each R1 and R2 is independently any nucleotide, non-nucleotide, or polynucleotide which can be naturally-occurring or chemically-modified, each X and Y is independently O, S, N, alkyl, or substituted alkyl, each Z and W is independently O, S, N, alkyl, substituted alkyl, O-alkyl, S-alkyl, alkaryl, or aralkyl, and wherein W, X, Y, and Z are optionally not all O.

The chemically-modified internucleotide linkages having Formula I, for example, wherein any Z, W, X, and/or Y independently comprises a sulphur atom, can be present in one or both oligonucleotide strands of the siNA duplex, for example, in the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) chemically-modified internucleotide linkages having Formula I at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the sense strand, the antisense strand, or both strands. For example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified internucleotide linkages having Formula I at the 5′-end of the sense strand, the antisense strand, or both strands. In another non-limiting example, an exemplary siNA molecule of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) pyrimidine nucleotides with chemically-modified internucleotide linkages having Formula I in the sense strand, the antisense strand, or both strands. In yet another non-limiting example, an exemplary siNA molecule of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) purine nucleotides with chemically-modified internucleotide linkages having Formula I in the sense strand, the antisense strand, or both strands. In another embodiment, a siNA molecule of the invention having internucleotide linkage(s) of Formula I also comprises a chemically-modified nucleotide or non-nucleotide having any of Formulae I-VII.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against a MAP kinase inside a cell or reconstituted in vitro system, wherein the chemical modification comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) nucleotides or non-nucleotides having Formula II:

wherein each R3, R4, R5, R6, R7, R8, R10, R11 and R12 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF₃, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-5-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or group having Formula I; R9 is O, S, CH2, S═O, CHF, or CF2, and B is a nucleosidic base such as adenine, guanine, uracil, cytosine, thymine, 2-aminoadenosine, 5-methylcytosine, 2,6-diaminopurine, or any other non-naturally occurring base that can be complementary or non-complementary to target RNA or a non-nucleosidic base such as phenyl, naphthyl, 3-nitropyrrole, 5-nitroindole, nebularine, pyridone, pyridinone, or any other non-naturally occurring universal base that can be complementary or non-complementary to target RNA.

The chemically-modified nucleotide or non-nucleotide of Formula II can be present in one or both oligonucleotide strands of the siNA duplex, for example in the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more chemically-modified nucleotide or non-nucleotide of Formula II at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the sense strand, the antisense strand, or both strands. For example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified nucleotides or non-nucleotides of Formula II at the 5′-end of the sense strand, the antisense strand, or both strands. In another non-limiting example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified nucleotides or non-nucleotides of Formula II at the 3′-end of the sense strand, the antisense strand, or both strands.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against a MAP kinase inside a cell or reconstituted in vitro system, wherein the chemical modification comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) nucleotides or non-nucleotides having Formula III:

wherein each R3, R4, R5, R6, R7, R8, R10, R11 and R12 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-5-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or group having Formula I; R9 is O, S, CH2, S═O, CHF, or CF2, and B is a nucleosidic base such as adenine, guanine, uracil, cytosine, thymine, 2-aminoadenosine, 5-methylcytosine, 2,6-diaminopurine, or any other non-naturally occurring base that can be employed to be complementary or non-complementary to target RNA or a non-nucleosidic base such as phenyl, naphthyl, 3-nitropyrrole, 5-nitroindole, nebularine, pyridone, pyridinone, or any other non-naturally occurring universal base that can be complementary or non-complementary to target RNA.

The chemically-modified nucleotide or non-nucleotide of Formula III can be present in one or both oligonucleotide strands of the siNA duplex, for example, in the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more chemically-modified nucleotide or non-nucleotide of Formula III at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the sense strand, the antisense strand, or both strands. For example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified nucleotide(s) or non-nucleotide(s) of Formula III at the 5′-end of the sense strand, the antisense strand, or both strands. In another non-limiting example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified nucleotide or non-nucleotide of Formula III at the 3′-end of the sense strand, the antisense strand, or both strands.

In another embodiment, a siNA molecule of the invention comprises a nucleotide having Formula II or III, wherein the nucleotide having Formula II or III is in an inverted configuration. For example, the nucleotide having Formula II or III is connected to the siNA construct in a 3′-3′,3′-2′,2′-3′, or 5′-5′ configuration, such as at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of one or both siNA strands.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against a MAP kinase inside a cell or reconstituted in vitro system, wherein the chemical modification comprises a 5′-terminal phosphate group having Formula IV:

wherein each X and Y is independently O, S, N, alkyl, substituted alkyl, or alkylhalo; wherein each Z and W is independently O, S, N, alkyl, substituted alkyl, O-alkyl, S-alkyl, alkaryl, aralkyl, or alkylhalo; and wherein W, X, Y and Z are not all O.

In one embodiment, the invention features a siNA molecule having a 5′-terminal phosphate group having Formula IV on the target-complementary strand, for example, a strand complementary to a target RNA, wherein the siNA molecule comprises an all RNA siNA molecule. In another embodiment, the invention features a siNA molecule having a 5′-terminal phosphate group having Formula IV on the target-complementary strand wherein the siNA molecule also comprises about 1 to about 3 (e.g., about 1, 2, or 3) nucleotide 3′-terminal nucleotide overhangs having about 1 to about 4 (e.g., about 1, 2, 3, or 4) deoxyribonucleotides on the 3′-end of one or both strands. In another embodiment, a 5′-terminal phosphate group having Formula IV is present on the target-complementary strand of a siNA molecule of the invention, for example a siNA molecule having chemical modifications having any of Formulae I-VII.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against a MAP kinase inside a cell or reconstituted in vitro system, wherein the chemical modification comprises one or more phosphorothioate internucleotide linkages. For example, in a non-limiting example, the invention features a chemically-modified short interfering nucleic acid (siNA) having about 1, 2, 3, 4, 5, 6, 7, 8 or more phosphorothioate internucleotide linkages in one siNA strand. In yet another embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) individually having about 1, 2, 3, 4, 5, 6, 7, 8 or more phosphorothioate internucleotide linkages in both siNA strands. The phosphorothioate internucleotide linkages can be present in one or both oligonucleotide strands of the siNA duplex, for example in the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more phosphorothioate internucleotide linkages at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the sense strand, the antisense strand, or both strands. For example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) consecutive phosphorothioate internucleotide linkages at the 5′-end of the sense strand, the antisense strand, or both strands. In another non-limiting example, an exemplary siNA molecule of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) pyrimidine phosphorothioate internucleotide linkages in the sense strand, the antisense strand, or both strands. In yet another non-limiting example, an exemplary siNA molecule of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) purine phosphorothioate internucleotide linkages in the sense strand, the antisense strand, or both strands.

In one embodiment, the invention features a siNA molecule, wherein the sense strand comprises one or more, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or about one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the sense strand; and wherein the antisense strand comprises about 1 to about 10 or more, specifically about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the antisense strand. In another embodiment, one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more, pyrimidine nucleotides of the sense and/or antisense siNA strand are chemically-modified with 2′-deoxy, 2′-O-methyl and/or 2′-deoxy-2′-fluoro nucleotides, with or without one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more, phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends, being present in the same or different strand.

In another embodiment, the invention features a siNA molecule, wherein the sense strand comprises about 1 to about 5, specifically about 1, 2, 3, 4, or 5 phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3-end, the 5′-end, or both of the 3′- and 5′-ends of the sense strand; and wherein the antisense strand comprises about 1 to about 5 or more, specifically about 1, 2, 3, 4, 5, or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the antisense strand. In another embodiment, one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more, pyrimidine nucleotides of the sense and/or antisense siNA strand are chemically-modified with 2′-deoxy, 2′-O-methyl and/or 2′-deoxy-2′-fluoro nucleotides, with or without about 1 to about 5 or more, for example about 1, 2, 3, 4, 5, or more phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends, being present in the same or different strand.

In one embodiment, the invention features a siNA molecule, wherein the sense strand comprises one or more, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more phosphorothioate internucleotide linkages, and/or about one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the sense strand; and wherein the antisense strand comprises about 1 to about 10 or more, specifically about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the antisense strand. In another embodiment, one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more pyrimidine nucleotides of the sense and/or antisense siNA strand are chemically-modified with 2′-deoxy, 2′-O-methyl and/or 2′-deoxy-2′-fluoro nucleotides, with or without one or more, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, or more phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends, being present in the same or different strand.

In another embodiment, the invention features a siNA molecule, wherein the sense strand comprises about 1 to about 5 or more, specifically about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the sense strand; and wherein the antisense strand comprises about 1 to about 5 or more, specifically about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2′-deoxy, 2′-O-methyl, 2′-deoxy-2′-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of the antisense strand. In another embodiment, one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more pyrimidine nucleotides of the sense and/or antisense siNA strand are chemically-modified with 2′-deoxy, 2′-O-methyl and/or 2′-deoxy-2′-fluoro nucleotides, with or without about 1 to about 5, for example about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends, being present in the same or different strand.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule having about 1 to about 5, specifically about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages in each strand of the siNA molecule.

In another embodiment, the invention features a siNA molecule comprising 2′-5′ internucleotide linkages. The 2′-5′ internucleotide linkage(s) can be at the 3′-end, the 5′-end, or both of the 3′- and 5′-ends of one or both siNA sequence strands. In addition, the 2′-5′ internucleotide linkage(s) can be present at various other positions within one or both siNA sequence strands, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more including every internucleotide linkage of a pyrimidine nucleotide in one or both strands of the siNA molecule can comprise a 2′-5′ internucleotide linkage, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more including every internucleotide linkage of a purine nucleotide in one or both strands of the siNA molecule can comprise a 2′-5′ internucleotide linkage.

In another embodiment, a chemically-modified siNA molecule of the invention comprises a duplex having two strands, one or both of which can be chemically-modified, wherein each strand is about 18 to about 27 (e.g., about 18, 19, 20, 21, 22, 23, 24, 25, 26, or 27) nucleotides in length, wherein the duplex has about 18 to about 23 (e.g., about 18, 19, 20, 21, 22, or 23) base pairs, and wherein the chemical modification comprises a structure having any of Formulae I-VII. For example, an exemplary chemically-modified siNA molecule of the invention comprises a duplex having two strands, one or both of which can be chemically-modified with a chemical modification having any of Formulae I-VII or any combination thereof, wherein each strand consists of about 21 nucleotides, each having a 2-nucleotide 3′-terminal nucleotide overhang, and wherein the duplex has about 19 base pairs. In another embodiment, a siNA molecule of the invention comprises a single stranded hairpin structure, wherein the siNA is about 36 to about 70 (e.g., about 36, 40, 45, 50, 55, 60, 65, or 70) nucleotides in length having about 18 to about 23 (e.g., about 18, 19, 20, 21, 22, or 23) base pairs, and wherein the siNA can include a chemical modification comprising a structure having any of Formulae I-VII or any combination thereof. For example, an exemplary chemically-modified siNA molecule of the invention comprises a linear oligonucleotide having about 42 to about 50 (e.g., about 42, 43, 44, 45, 46, 47, 48, 49, or 50) nucleotides that is chemically-modified with a chemical modification having any of Formulae I-VII or any combination thereof, wherein the linear oligonucleotide forms a hairpin structure having about 19 base pairs and a 2-nucleotide 3′-terminal nucleotide overhang. In another embodiment, a linear hairpin siNA molecule of the invention contains a stem loop motif, wherein the loop portion of the siNA molecule is biodegradable. For example, a linear hairpin siNA molecule of the invention is designed such that degradation of the loop portion of the siNA molecule in vivo can generate a double-stranded siNA molecule with 3′-terminal overhangs, such as 3′-terminal nucleotide overhangs comprising about 2 nucleotides.

In another embodiment, a siNA molecule of the invention comprises a circular nucleic acid molecule, wherein the siNA is about 38 to about 70 (e.g., about 38, 40, 45, 50, 55, 60, 65, or 70) nucleotides in length having about 18 to about 23 (e.g., about 18, 19, 20, 21, 22, or 23) base pairs, and wherein the siNA can include a chemical modification, which comprises a structure having any of Formulae I-VII or any combination thereof. For example, an exemplary chemically-modified siNA molecule of the invention comprises a circular oligonucleotide having about 42 to about 50 (e.g., about 42, 43, 44, 45, 46, 47, 48, 49, or 50) nucleotides that is chemically-modified with a chemical modification having any of Formulae I-VII or any combination thereof, wherein the circular oligonucleotide forms a dumbbell shaped structure having about 19 base pairs and 2 loops.

In another embodiment, a circular siNA molecule of the invention contains two loop motifs, wherein one or both loop portions of the siNA molecule is biodegradable. For example, a circular siNA molecule of the invention is designed such that degradation of the loop portions of the siNA molecule in vivo can generate a double-stranded siNA molecule with 3′-terminal overhangs, such as 3′-terminal nucleotide overhangs comprising about 2 nucleotides.

In one embodiment, a siNA molecule of the invention comprises at least one (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) abasic moiety, for example a compound having Formula V:

wherein each R3, R4, R5, R6, R7, R8, R10, R11, R12, and R13 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-5-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or group having Formula I; R9 is O, S, CH2, S═O, CHF, or CF2.

In one embodiment, a siNA molecule of the invention comprises at least one (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) inverted abasic moiety, for example a compound having Formula VI:

wherein each R3, R4, R5, R6, R7, R8, R10, R11, R12, and R13 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-5-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or group having Formula I; R9 is O, S, CH2, S═O, CHF, or CF2, and either R2, R3, R8 or R13 serve as points of attachment to the siNA molecule of the invention.

In another embodiment, a siNA molecule of the invention comprises at least one (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) substituted polyalkyl moieties, for example a compound having Formula VII:

wherein each n is independently an integer from 1 to 12, each R1, R2 and R3 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-5-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or a group having Formula I, and R1, R2 or R3 serves as points of attachment to the siNA molecule of the invention.

In another embodiment, the invention features a compound having Formula VII, wherein R1 and R2 are hydroxyl (OH) groups, n=1, and R3 comprises 0 and is the point of attachment to the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of one or both strands of a double-stranded siNA molecule of the invention or to a single-stranded siNA molecule of the invention. This modification is referred to herein as “glyceryl” (for example modification 6 in FIG. 10).

In another embodiment, a moiety having any of Formula V, VI or VII of the invention is at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of a siNA molecule of the invention. For example, a moiety having Formula V, VI or VII can be present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the antisense strand, the sense strand, or both antisense and sense strands of the siNA molecule. In addition, a moiety having Formula VII can be present at the 3′-end or the 5′-end of a hairpin siNA molecule as described herein.

In another embodiment, a siNA molecule of the invention comprises an abasic residue having Formula V or VI, wherein the abasic residue having Formula VI or VI is connected to the siNA construct in a 3′-3′,3′-2′,2′-3′, or 5′-5′ configuration, such as at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of one or both siNA strands.

In one embodiment, a siNA molecule of the invention comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) locked nucleic acid (LNA) nucleotides, for example at the 5′-end, the 3′-end, both of the 5′ and 3′-ends, or any combination thereof, of the siNA molecule.

In another embodiment, a siNA molecule of the invention comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) acyclic nucleotides, for example at the 5′-end, the 3′-end, both of the 5′ and 3′-ends, or any combination thereof, of the siNA molecule.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically-modified siNA comprises a sense region, where any (e.g., one or more or all) pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and where any (e.g., one or more or all) purine nucleotides present in the sense region are 2′-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2′-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2′-deoxy purine nucleotides).

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically-modified siNA comprises a sense region, where any (e.g., one or more or all) pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and where any (e.g., one or more or all) purine nucleotides present in the sense region are 2′-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2′-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2′-deoxy purine nucleotides), wherein any nucleotides comprising a 3′-terminal nucleotide overhang that are present in said sense region are 2′-deoxy nucleotides.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically-modified siNA comprises a sense region, where any (e.g., one or more or all) pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and where any (e.g., one or more or all) purine nucleotides present in the sense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides).

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically-modified siNA comprises a sense region, where any (e.g., one or more or all) pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and where any (e.g., one or more or all) purine nucleotides present in the sense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides), wherein any nucleotides comprising a 3′-terminal nucleotide overhang that are present in said sense region are 2′-deoxy nucleotides.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically-modified siNA comprises an antisense region, where any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides).

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically-modified siNA comprises an antisense region, where any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides), wherein any nucleotides comprising a 3′-terminal nucleotide overhang that are present in said antisense region are 2′-deoxy nucleotides.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically-modified siNA comprises an antisense region, where any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and where any (e.g., one or more or all) purine nucleotides present in the antisense region are 2′-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2′-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2′-deoxy purine nucleotides).

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention, wherein the chemically-modified siNA comprises an antisense region, where any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and where any (e.g., one or more or all) purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides).

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention capable of mediating RNA interference (RNAi) against a MAP kinase inside a cell or reconstituted in vitro system, wherein the chemically-modified siNA comprises a sense region, where one or more pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and where one or more purine nucleotides present in the sense region are 2′-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2′-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2′-deoxy purine nucleotides), and inverted deoxy abasic modifications that are optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the sense region, the sense region optionally further comprising a 3′-terminal overhang having about 1 to about 4 (e.g., about 1, 2, 3, or 4) 2′-deoxyribonucleotides; and wherein the chemically-modified short interfering nucleic acid molecule comprises an antisense region, where one or more pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein one or more purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides), and a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the antisense sequence, the antisense region optionally further comprising a 3′-terminal nucleotide overhang having about 1 to about 4 (e.g., about 1, 2, 3, or 4) 2′-deoxynucleotides, wherein the overhang nucleotides can further comprise one or more (e.g., 1, 2, 3, or 4) phosphorothioate internucleotide linkages. Non-limiting examples of these chemically-modified siNAs are shown in FIGS. 4 and 5 and Tables III and IV herein.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention capable of mediating RNA interference (RNAi) against a MAP kinase inside a cell or reconstituted in vitro system, wherein the chemically-modified siNA comprises a sense region, where one or more pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and where one or more purine nucleotides present in the sense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides), and inverted deoxy abasic modifications that are optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the sense region, the sense region optionally further comprising a 3′-terminal overhang having about 1 to about 4 (e.g., about 1, 2, 3, or 4) 2′-deoxyribonucleotides; and wherein the chemically-modified short interfering nucleic acid molecule comprises an antisense region, where one or more pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein one or more purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides), and a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the antisense sequence, the antisense region optionally further comprising a 3′-terminal nucleotide overhang having about 1 to about 4 (e.g., about 1, 2, 3, or 4) 2′-deoxynucleotides, wherein the overhang nucleotides can further comprise one or more (e.g., 1, 2, 3, or 4) phosphorothioate internucleotide linkages. Non-limiting examples of these chemically-modified siNAs are shown in FIGS. 4 and 5 and Tables III and IV herein.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention capable of mediating RNA interference (RNAi) against a MAP kinase inside a cell or reconstituted in vitro system, wherein the siNA comprises a sense region, where one or more pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and where one or more purine nucleotides present in the sense region are purine ribonucleotides (e.g., wherein all purine nucleotides are purine ribonucleotides or alternately a plurality of purine nucleotides are purine ribonucleotides), and inverted deoxy abasic modifications that are optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the sense region, the sense region optionally further comprising a 3′-terminal overhang having about 1 to about 4 (e.g., about 1, 2, 3, or 4) 2′-deoxyribonucleotides; and wherein the siNA comprises an antisense region, where one or more pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides), and a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the antisense sequence, the antisense region optionally further comprising a 3′-terminal nucleotide overhang having about 1 to about 4 (e.g., about 1, 2, 3, or 4) 2′-deoxynucleotides, wherein the overhang nucleotides can further comprise one or more (e.g., 1, 2, 3, or 4) phosphorothioate internucleotide linkages. Non-limiting examples of these chemically-modified siNAs are shown in FIGS. 4 and 5 and Tables III and IV herein.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention capable of mediating RNA interference (RNAi) against a MAP kinase inside a cell or reconstituted in vitro system, wherein the chemically-modified siNA comprises a sense region, where one or more pyrimidine nucleotides present in the sense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and for example where one or more purine nucleotides present in the sense region are selected from the group consisting of 2′-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides (e.g., wherein all purine nucleotides are selected from the group consisting of 2′-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides or alternately a plurality of purine nucleotides are selected from the group consisting of 2′-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides), and wherein inverted deoxy abasic modifications are optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the sense region, the sense region optionally further comprising a 3′-terminal overhang having about 1 to about 4 (e.g., about 1, 2, 3, or 4) 2′-deoxyribonucleotides; and wherein the chemically-modified short interfering nucleic acid molecule comprises an antisense region, where one or more pyrimidine nucleotides present in the antisense region are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein one or more purine nucleotides present in the antisense region are selected from the group consisting of 2′-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides (e.g., wherein all purine nucleotides are selected from the group consisting of 2′-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides or alternately a plurality of purine nucleotides are selected from the group consisting of 2′-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2′-methoxyethyl nucleotides, 4′-thionucleotides, and 2′-O-methyl nucleotides), and a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the antisense sequence, the antisense region optionally further comprising a 3′-terminal nucleotide overhang having about 1 to about 4 (e.g., about 1, 2, 3, or 4) 2′-deoxynucleotides, wherein the overhang nucleotides can further comprise one or more (e.g., 1, 2, 3, or 4) phosphorothioate internucleotide linkages.

In another embodiment, any modified nucleotides present in the siNA molecules of the invention, preferably in the antisense strand of the siNA molecules of the invention, but also optionally in the sense and/or both antisense and sense strands, comprise modified nucleotides having properties or characteristics similar to naturally occurring ribonucleotides. For example, the invention features siNA molecules including modified nucleotides having a Northern conformation (e.g., Northern pseudorotation cycle, see for example Saenger, Principles of Nucleic Acid Structure, Springer-Verlag ed., 1984). As such, chemically modified nucleotides present in the siNA molecules of the invention, preferably in the antisense strand of the siNA molecules of the invention, but also optionally in the sense and/or both antisense and sense strands, are resistant to nuclease degradation while at the same time maintaining the capacity to mediate RNAi. Non-limiting examples of nucleotides having a northern configuration include locked nucleic acid (LNA) nucleotides (e.g., 2′-O, 4′-C-methylene-(D-ribofuranosyl) nucleotides); 2′-methoxyethoxy (MOE) nucleotides; 2′-methyl-thio-ethyl, 2′-deoxy-2′-fluoro nucleotides, 2′-deoxy-2′-chloro nucleotides, 2′-azido nucleotides, and 2′-O-methyl nucleotides.

In one embodiment, the invention features a chemically-modified short interfering nucleic acid molecule (siNA) capable of mediating RNA interference (RNAi) against a MAP kinase inside a cell or reconstituted in vitro system, wherein the chemical modification comprises a conjugate covalently attached to the chemically-modified siNA molecule. In another embodiment, the conjugate is covalently attached to the chemically-modified siNA molecule via a biodegradable linker. In one embodiment, the conjugate molecule is attached at the 3′-end of either the sense strand, the antisense strand, or both strands of the chemically-modified siNA molecule. In another embodiment, the conjugate molecule is attached at the 5′-end of either the sense strand, the antisense strand, or both strands of the chemically-modified siNA molecule. In yet another embodiment, the conjugate molecule is attached both the 3′-end and 5′-end of either the sense strand, the antisense strand, or both strands of the chemically-modified siNA molecule, or any combination thereof. In one embodiment, a conjugate molecule of the invention comprises a molecule that facilitates delivery of a chemically-modified siNA molecule into a biological system, such as a cell. In another embodiment, the conjugate molecule attached to the chemically-modified siNA molecule is a polyethylene glycol, human serum albumin, or a ligand for a cellular receptor that can mediate cellular uptake. Examples of specific conjugate molecules contemplated by the instant invention that can be attached to chemically-modified siNA molecules are described in Vargeese et al., U.S. Ser. No. 10/201,394, incorporated by reference herein. The type of conjugates used and the extent of conjugation of siNA molecules of the invention can be evaluated for improved pharmacokinetic profiles, bioavailability, and/or stability of siNA constructs while at the same time maintaining the ability of the siNA to mediate RNAi activity. As such, one skilled in the art can screen siNA constructs that are modified with various conjugates to determine whether the siNA conjugate complex possesses improved properties while maintaining the ability to mediate RNAi, for example, in animal models as are generally known in the art.

In one embodiment, the invention features a short interfering nucleic acid (siNA) molecule of the invention, wherein the siNA further comprises a nucleotide, non-nucleotide, or mixed nucleotide/non-nucleotide linker that joins the sense region of the siNA to the antisense region of the siNA. In one embodiment, a nucleotide linker of the invention can be a linker of ≧2 nucleotides in length, for example 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides in length. In another embodiment, the nucleotide linker can be a nucleic acid aptamer. By “aptamer” or “nucleic acid aptamer” as used herein is meant a nucleic acid molecule that binds specifically to a target molecule wherein the nucleic acid molecule has sequence that comprises a sequence recognized by the target molecule in its natural setting. Alternately, an aptamer can be a nucleic acid molecule that binds to a target molecule where the target molecule does not naturally bind to a nucleic acid. The target molecule can be any molecule of interest. For example, the aptamer can be used to bind to a ligand-binding domain of a protein, thereby preventing interaction of the naturally occurring ligand with the protein. This is a non-limiting example and those in the art will recognize that other embodiments can be readily generated using techniques generally known in the art. (See, for example, Gold et al., 1995, Annu. Rev. Biochem., 64, 763; Brody and Gold, 2000, J. Biotechnol., 74, 5; Sunday, 2000, Curr. Opin. Mol. Ther., 2, 100; Kusser, 2000, J. Biotechnol., 74, 27; Hermann and Patel, 2000, Science, 287, 820; and Jayasena, 1999, Clinical Chemistry, 45, 1628.)

In yet another embodiment, a non-nucleotide linker of the invention comprises abasic nucleotide, polyether, polyamine, polyamide, peptide, carbohydrate, lipid, polyhydrocarbon, or other polymeric compounds (e.g. polyethylene glycols such as those having between 2 and 100 ethylene glycol units). Specific examples include those described by Seela and Kaiser, Nucleic Acids Res. 1990, 18:6353 and Nucleic Acids Res. 1987, 15:3113; Cload and Schepartz, J. Am. Chem. Soc. 1991, 113:6324; Richardson and Schepartz, J. Am. Chem. Soc. 1991, 113:5109; Ma et al., Nucleic Acids Res. 1993, 21:2585 and Biochemistry 1993, 32:1751; Durand et al., Nucleic Acids Res. 1990, 18:6353; McCurdy et al., Nucleosides & Nucleotides 1991, 10:287; Jschke et al., Tetrahedron Lett. 1993, 34:301; Ono et al., Biochemistry 1991, 30:9914; Arnold et al., International Publication No. WO 89/02439; Usman et al., International Publication No. WO 95/06731; Dudycz et al., International Publication No. WO 95/11910 and Ferentz and Verdine, J. Am. Chem. Soc. 1991, 113:4000, all hereby incorporated by reference herein. A “non-nucleotide” further means any group or compound that can be incorporated into a nucleic acid chain in the place of one or more nucleotide units, including either sugar and/or phosphate substitutions, and allows the remaining bases to exhibit their enzymatic activity. The group or compound can be abasic in that it does not contain a commonly recognized nucleotide base, such as adenosine, guanine, cytosine, uracil or thymine, for example at the C1 position of the sugar.

In one embodiment, the invention features a short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) inside a cell or reconstituted in vitro system, wherein one or both strands of the siNA molecule that are assembled from two separate oligonucleotides do not comprise any ribonucleotides. For example, a siNA molecule can be assembled from a single oligonucleotide where the sense and antisense regions of the siNA comprise separate oligonucleotides that do not have any ribonucleotides (e.g., nucleotides having a 2′-OH group) present in the oligonucleotides. In another example, a siNA molecule can be assembled from a single oligonucleotide where the sense and antisense regions of the siNA are linked or circularized by a nucleotide or non-nucleotide linker as described herein, wherein the oligonucleotide does not have any ribonucleotides (e.g., nucleotides having a 2′-OH group) present in the oligonucleotide. Applicant has surprisingly found that the presence of ribonucleotides (e.g., nucleotides having a 2′-hydroxyl group) within the siNA molecule is not required or essential to support RNAi activity. As such, in one embodiment, all positions within the siNA can include chemically modified nucleotides and/or non-nucleotides such as nucleotides and or non-nucleotides having Formula I, II, III, IV, V, VI, or VII or any combination thereof to the extent that the ability of the siNA molecule to support RNAi activity in a cell is maintained.

In one embodiment, a siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system, wherein the siNA molecule comprises a single stranded polynucleotide having complementarity to a target nucleic acid sequence. In another embodiment, the single stranded siNA molecule of the invention comprises a 5′-terminal phosphate group. In another embodiment, the single stranded siNA molecule of the invention comprises a 5′-terminal phosphate group and a 3′-terminal phosphate group (e.g., a 2′,3′-cyclic phosphate). In another embodiment, the single stranded siNA molecule of the invention comprises about 19 to about 29 nucleotides. In yet another embodiment, the single stranded siNA molecule of the invention comprises one or more chemically modified nucleotides or non-nucleotides described herein. For example, all the positions within the siNA molecule can include chemically-modified nucleotides such as nucleotides having any of Formulae I-VII, or any combination thereof to the extent that the ability of the siNA molecule to support RNAi activity in a cell is maintained.

In one embodiment, a siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system, wherein the siNA molecule comprises a single stranded polynucleotide having complementarity to a target nucleic acid sequence, and wherein one or more pyrimidine nucleotides present in the siNA are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any purine nucleotides present in the antisense region are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides), and a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the antisense sequence, the siNA optionally further comprising about 1 to about 4 (e.g., about 1, 2, 3, or 4) terminal 2′-deoxynucleotides at the 3′-end of the siNA molecule, wherein the terminal nucleotides can further comprise one or more (e.g., 1, 2, 3, or 4) phosphorothioate internucleotide linkages, and wherein the siNA optionally further comprises a terminal phosphate group, such as a 5′-terminal phosphate group.

In one embodiment, a siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system, wherein the siNA molecule comprises a single stranded polynucleotide having complementarity to a target nucleic acid sequence, and wherein one or more pyrimidine nucleotides present in the siNA are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any purine nucleotides present in the siNA are 2′-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-O-methyl purine nucleotides), and a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the antisense sequence, the siNA optionally further comprising about 1 to about 4 (e.g., about 1, 2, 3, or 4) terminal 2′-deoxynucleotides at the 3′-end of the siNA molecule, wherein the terminal nucleotides can further comprise one or more (e.g., 1, 2, 3, or 4) phosphorothioate internucleotide linkages, and wherein the siNA optionally further comprises a terminal phosphate group, such as a 5′-terminal phosphate group.

In one embodiment, a siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system, wherein the siNA molecule comprises a single stranded polynucleotide having complementarity to a target nucleic acid sequence, and wherein one or more pyrimidine nucleotides present in the siNA are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any purine nucleotides present in the siNA are 2′-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2′-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2′-deoxy purine nucleotides), and a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the antisense sequence, the siNA optionally further comprising about 1 to about 4 (e.g., about 1, 2, 3, or 4) terminal 2′-deoxynucleotides at the 3′-end of the siNA molecule, wherein the terminal nucleotides can further comprise one or more (e.g., 1, 2, 3, or 4) phosphorothioate internucleotide linkages, and wherein the siNA optionally further comprises a terminal phosphate group, such as a 5′-terminal phosphate group.

In one embodiment, a siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system, wherein the siNA molecule comprises a single stranded polynucleotide having complementarity to a target nucleic acid sequence, and wherein one or more pyrimidine nucleotides present in the siNA are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any purine nucleotides present in the siNA are locked nucleic acid (LNA) nucleotides (e.g., wherein all purine nucleotides are LNA nucleotides or alternately a plurality of purine nucleotides are LNA nucleotides), and a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the antisense sequence, the siNA optionally further comprising about 1 to about 4 (e.g., about 1, 2, 3, or 4) terminal 2′-deoxynucleotides at the 3′-end of the siNA molecule, wherein the terminal nucleotides can further comprise one or more (e.g., 1, 2, 3, or 4) phosphorothioate internucleotide linkages, and wherein the siNA optionally further comprises a terminal phosphate group, such as a 5′-terminal phosphate group.

In one embodiment, a siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system, wherein the siNA molecule comprises a single stranded polynucleotide having complementarity to a target nucleic acid sequence, and wherein one or more pyrimidine nucleotides present in the siNA are 2′-deoxy-2′-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2′-deoxy-2′-fluoro pyrimidine nucleotides), and wherein any purine nucleotides present in the siNA are 2′-methoxyethyl purine nucleotides (e.g., wherein all purine nucleotides are 2′-methoxyethyl purine nucleotides or alternately a plurality of purine nucleotides are 2′-methoxyethyl purine nucleotides), and a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3′-end, the 5′-end, or both of the 3′ and 5′-ends of the antisense sequence, the siNA optionally further comprising about 1 to about 4 (e.g., about 1, 2, 3, or 4) terminal 2′-deoxynucleotides at the 3′-end of the siNA molecule, wherein the terminal nucleotides can further comprise one or more (e.g., 1, 2, 3, or 4) phosphorothioate internucleotide linkages, and wherein the siNA optionally further comprises a terminal phosphate group, such as a 5′-terminal phosphate group.

In another embodiment, any modified nucleotides present in the single stranded siNA molecules of the invention comprise modified nucleotides having properties or characteristics similar to naturally occurring ribonucleotides. For example, the invention features siNA molecules including modified nucleotides having a Northern conformation (e.g., Northern pseudorotation cycle, see for example Saenger, Principles of Nucleic Acid Structure, Springer-Verlag ed., 1984). As such, chemically modified nucleotides present in the single stranded siNA molecules of the invention are preferably resistant to nuclease degradation while at the same time maintaining the capacity to mediate RNAi.

In one embodiment, the invention features a method for modulating the expression of a MAP kinase gene within a cell comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the MAP kinase gene; and (b) introducing the siNA molecule into a cell under conditions suitable to modulate the expression of the MAP kinase gene in the cell.

In one embodiment, the invention features a method for modulating the expression of a MAP kinase gene within a cell comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the MAP kinase gene and wherein the sense strand sequence of the siNA comprises a sequence identical to the sequence of the target RNA; and (b) introducing the siNA molecule into a cell under conditions suitable to modulate the expression of the MAP kinase gene in the cell.

In another embodiment, the invention features a method for modulating the expression of more than one MAP kinase gene within a cell comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the MAP kinase genes; and (b) introducing the siNA molecules into a cell under conditions suitable to modulate the expression of the MAP kinase genes in the cell.

In another embodiment, the invention features a method for modulating the expression of more than one MAP kinase gene within a cell comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the MAP kinase gene and wherein the sense strand sequence of the siNA comprises a sequence identical to the sequence of the target RNA; and (b) introducing the siNA molecules into a cell under conditions suitable to modulate the expression of the MAP kinase genes in the cell.

In one embodiment, siNA molecules of the invention are used as reagents in ex vivo applications. For example, siNA reagents are introduced into tissue or cells that are transplanted into a subject for therapeutic effect. The cells and/or tissue can be derived from an organism or subject that later receives the explant, or can be derived from another organism or subject prior to transplantation. The siNA molecules can be used to modulate the expression of one or more genes in the cells or tissue, such that the cells or tissue obtain a desired phenotype or are able to perform a function when transplanted in vivo. In one embodiment, certain target cells from a patient are extracted. These extracted cells are contacted with siNAs targeting a specific nucleotide sequence within the cells under conditions suitable for uptake of the siNAs by these cells (e.g. using delivery reagents such as cationic lipids, liposomes and the like or using techniques such as electroporation to facilitate the delivery of siNAs into cells). The cells are then reintroduced back into the same patient or other patients. In one embodiment, the invention features a method of modulating the expression of a MAP kinase gene in a tissue explant comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the MAP kinase gene; and (b) introducing the siNA molecule into a cell of the tissue explant derived from a particular organism under conditions suitable to modulate the expression of the MAP kinase gene in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the organism the tissue was derived from or into another organism under conditions suitable to modulate the expression of the MAP kinase gene in that organism.

In one embodiment, the invention features a method of modulating the expression of a MAP kinase gene in a tissue explant comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the MAP kinase gene and wherein the sense strand sequence of the siNA comprises a sequence identical to the sequence of the target RNA; and (b) introducing the siNA molecule into a cell of the tissue explant derived from a particular organism under conditions suitable to modulate the expression of the MAP kinase gene in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the organism the tissue was derived from or into another organism under conditions suitable to modulate the expression of the MAP kinase gene in that organism.

In another embodiment, the invention features a method of modulating the expression of more than one MAP kinase gene in a tissue explant comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the MAP kinase genes; and (b) introducing the siNA molecules into a cell of the tissue explant derived from a particular organism under conditions suitable to modulate the expression of the MAP kinase genes in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the organism the tissue was derived from or into another organism under conditions suitable to modulate the expression of the MAP kinase genes in that organism.

In one embodiment, the invention features a method of modulating the expression of a MAP kinase gene in an organism comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the MAP kinase gene; and (b) introducing the siNA molecule into the organism under conditions suitable to modulate the expression of the MAP kinase gene in the organism.

In another embodiment, the invention features a method of modulating the expression of more than one MAP kinase gene in an organism comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the MAP kinase genes; and (b) introducing the siNA molecules into the organism under conditions suitable to modulate the expression of the MAP kinase genes in the organism.

In one embodiment, the invention features a method for modulating the expression of a MAP kinase gene within a cell comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the MAP kinase gene; and (b) introducing the siNA molecule into a cell under conditions suitable to modulate the expression of the MAP kinase gene in the cell.

In another embodiment, the invention features a method for modulating the expression of more than one MAP kinase gene within a cell comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the MAP kinase gene; and (b) contacting the siNA molecule with a cell in vitro or in vivo under conditions suitable to modulate the expression of the MAP kinase genes in the cell.

In one embodiment, the invention features a method of modulating the expression of a MAP kinase gene in a tissue explant comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the MAP kinase gene; and (b) contacting the siNA molecule with a cell of the tissue explant derived from a particular organism under conditions suitable to modulate the expression of the MAP kinase gene in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the organism the tissue was derived from or into another organism under conditions suitable to modulate the expression of the MAP kinase gene in that organism.

In another embodiment, the invention features a method of modulating the expression of more than one MAP kinase gene in a tissue explant comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the MAP kinase gene; and (b) introducing the siNA molecules into a cell of the tissue explant derived from a particular organism under conditions suitable to modulate the expression of the MAP kinase genes in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the organism the tissue was derived from or into another organism under conditions suitable to modulate the expression of the MAP kinase genes in that organism.

In one embodiment, the invention features a method of modulating the expression of a MAP kinase gene in an organism comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the MAP kinase gene; and (b) introducing the siNA molecule into the organism under conditions suitable to modulate the expression of the MAP kinase gene in the organism.

In another embodiment, the invention features a method of modulating the expression of more than one MAP kinase gene in an organism comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the MAP kinase gene; and (b) introducing the siNA molecules into the organism under conditions suitable to modulate the expression of the MAP kinase genes in the organism.

In one embodiment, the invention features a method of modulating the expression of a MAP kinase gene in an organism comprising contacting the organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the MAP kinase gene in the organism.

In another embodiment, the invention features a method of modulating the expression of more than one MAP kinase gene in an organism comprising contacting the organism with one or more siNA molecules of the invention under conditions suitable to modulate the expression of the MAP kinase genes in the organism.

The siNA molecules of the invention can be designed to down-regulate or inhibit target (MAP kinase) gene expression through RNAi targeting of a variety of RNA molecules. In one embodiment, the siNA molecules of the invention are used to target various RNAs corresponding to a target gene. Non-limiting examples of such RNAs include messenger RNA (mRNA), alternate RNA splice variants of target gene(s), post-transcriptionally modified RNA of target gene(s), pre-mRNA of target gene(s), and/or RNA templates. If alternate splicing produces a family of transcripts that are distinguished by usage of appropriate exons, the instant invention can be used to inhibit gene expression through the appropriate exons to specifically inhibit or to distinguish among the functions of gene family members. For example, a protein that contains an alternatively spliced transmembrane domain can be expressed in both membrane bound and secreted forms. Use of the invention to target the exon containing the transmembrane domain can be used to determine the functional consequences of pharmaceutical targeting of membrane bound as opposed to the secreted form of the protein. Non-limiting examples of applications of the invention relating to targeting these RNA molecules include therapeutic pharmaceutical applications, pharmaceutical discovery applications, molecular diagnostic and gene function applications, and gene mapping, for example using single nucleotide polymorphism mapping with siNA molecules of the invention. Such applications can be implemented using known gene sequences or from partial sequences available from an expressed sequence tag (EST).

In another embodiment, the siNA molecules of the invention are used to target conserved sequences corresponding to a gene family or gene families such as MAP kinase family genes. As such, siNA molecules targeting multiple MAP kinase targets can provide increased therapeutic effect. In addition, siNA can be used to characterize pathways of gene function in a variety of applications. For example, the present invention can be used to inhibit the activity of target gene(s) in a pathway to determine the function of uncharacterized gene(s) in gene function analysis, mRNA function analysis, or translational analysis. The invention can be used to determine potential target gene pathways involved in various diseases and conditions toward pharmaceutical development. The invention can be used to understand pathways of gene expression involved in, for example, the progression and/or maintenance of cancer.

In one embodiment, siNA molecule(s) and/or methods of the invention are used to down-regulate the expression of gene(s) that encode RNA referred to by Genbank Accession, for example MAP kinase genes encoding RNA sequence(s) referred to herein by Genbank Accession number, for example, Genbank Accession Nos. shown in Table I.

In one embodiment, the invention features a method comprising: (a) generating a library of siNA constructs having a predetermined complexity; and (b) assaying the siNA constructs of (a) above, under conditions suitable to determine RNAi target sites within the target RNA sequence. In one embodiment, the siNA molecules of (a) have strands of a fixed length, for example, about 23 nucleotides in length. In another embodiment, the siNA molecules of (a) are of differing length, for example having strands of about 19 to about 25 (e.g., about 19, 20, 21, 22, 23, 24, or 25) nucleotides in length. In one embodiment, the assay can comprise a reconstituted in vitro siNA assay as described herein. In another embodiment, the assay can comprise a cell culture system in which target RNA is expressed. In another embodiment, fragments of target RNA are analyzed for detectable levels of cleavage, for example by gel electrophoresis, northern blot analysis, or RNAse protection assays, to determine the most suitable target site(s) within the target RNA sequence. The target RNA sequence can be obtained as is known in the art, for example, by cloning and/or transcription for in vitro systems, and by cellular expression in in vivo systems.

In one embodiment, the invention features a method comprising: (a) generating a randomized library of siNA constructs having a predetermined complexity, such as of 4N, where N represents the number of base paired nucleotides in each of the siNA construct strands (eg. for a siNA construct having 21 nucleotide sense and antisense strands with 19 base pairs, the complexity would be 419); and (b) assaying the siNA constructs of (a) above, under conditions suitable to determine RNAi target sites within the target MAP kinase RNA sequence. In another embodiment, the siNA molecules of (a) have strands of a fixed length, for example about 23 nucleotides in length. In yet another embodiment, the siNA molecules of (a) are of differing length, for example having strands of about 19 to about 25 (e.g., about 19, 20, 21, 22, 23, 24, or 25) nucleotides in length. In one embodiment, the assay can comprise a reconstituted in vitro siNA assay as described in Example 7 herein. In another embodiment, the assay can comprise a cell culture system in which target RNA is expressed. In another embodiment, fragments of MAP kinase RNA are analyzed for detectable levels of cleavage, for example by gel electrophoresis, northern blot analysis, or RNAse protection assays, to determine the most suitable target site(s) within the target MAP kinase RNA sequence. The target MAP kinase RNA sequence can be obtained as is known in the art, for example, by cloning and/or transcription for in vitro systems, and by cellular expression in in vivo systems.

In another embodiment, the invention features a method comprising: (a) analyzing the sequence of a RNA target encoded by a target gene; (b) synthesizing one or more sets of siNA molecules having sequence complementary to one or more regions of the RNA of (a); and (c) assaying the siNA molecules of (b) under conditions suitable to determine RNAi targets within the target RNA sequence. In one embodiment, the siNA molecules of (b) have strands of a fixed length, for example about 23 nucleotides in length. In another embodiment, the siNA molecules of (b) are of differing length, for example having strands of about 19 to about 25 (e.g., about 19, 20, 21, 22, 23, 24, or 25) nucleotides in length. In one embodiment, the assay can comprise a reconstituted in vitro siNA assay as described herein. In another embodiment, the assay can comprise a cell culture system in which target RNA is expressed. Fragments of target RNA are analyzed for detectable levels of cleavage, for example by gel electrophoresis, northern blot analysis, or RNAse protection assays, to determine the most suitable target site(s) within the target RNA sequence. The target RNA sequence can be obtained as is known in the art, for example, by cloning and/or transcription for in vitro systems, and by expression in in vivo systems.

By “target site” is meant a sequence within a target RNA that is “targeted” for cleavage mediated by a siNA construct which contains sequences within its antisense region that are complementary to the target sequence.

By “detectable level of cleavage” is meant cleavage of target RNA (and formation of cleaved product RNAs) to an extent sufficient to discern cleavage products above the background of RNAs produced by random degradation of the target RNA. Production of cleavage products from 1-5% of the target RNA is sufficient to detect above the background for most methods of detection.

In one embodiment, the invention features a composition comprising a siNA molecule of the invention, which can be chemically-modified, in a pharmaceutically acceptable carrier or diluent. In another embodiment, the invention features a pharmaceutical composition comprising siNA molecules of the invention, which can be chemically-modified, targeting one or more genes in a pharmaceutically acceptable carrier or diluent. In another embodiment, the invention features a method for diagnosing a disease or condition in a subject comprising administering to the subject a composition of the invention under conditions suitable for the diagnosis of the disease or condition in the subject. In another embodiment, the invention features a method for treating or preventing a disease or condition in a subject, comprising administering to the subject a composition of the invention under conditions suitable for the treatment or prevention of the disease or condition in the subject, alone or in conjunction with one or more other therapeutic compounds. In yet another embodiment, the invention features a method for reducing or preventing tissue rejection in a subject comprising administering to the subject a composition of the invention under conditions suitable for the reduction or prevention of tissue rejection in the subject.

In another embodiment, the invention features a method for validating a MAP kinase gene target comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands includes a sequence complementary to RNA of a MAP kinase target gene; (b) introducing the siNA molecule into a cell, tissue, or organism under conditions suitable for modulating expression of the MAP kinase target gene in the cell, tissue, or organism; and (c) determining the function of the gene by assaying for any phenotypic change in the cell, tissue, or organism.

In another embodiment, the invention features a method for validating a MAP kinase target comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands includes a sequence complementary to RNA of a MAP kinase target gene; (b) introducing the siNA molecule into a biological system under conditions suitable for modulating expression of the MAP kinase target gene in the biological system; and (c) determining the function of the gene by assaying for any phenotypic change in the biological system.

By “biological system” is meant, material, in a purified or unpurified form, from biological sources, including but not limited to human, animal, plant, insect, bacterial, viral or other sources, wherein the system comprises the components required for RNAi activity. The term “biological system” includes, for example, a cell, tissue, or organism, or extract thereof. The term biological system also includes reconstituted RNAi systems that can be used in an in vitro setting.

By “phenotypic change” is meant any detectable change to a cell that occurs in response to contact or treatment with a nucleic acid molecule of the invention (e.g., siNA). Such detectable changes include, but are not limited to, changes in shape, size, proliferation, motility, protein expression or RNA expression or other physical or chemical changes as can be assayed by methods known in the art. The detectable change can also include expression of reporter genes/molecules such as Green Florescent Protein (GFP) or various tags that are used to identify an expressed protein or any other cellular component that can be assayed.

In one embodiment, the invention features a kit containing a siNA molecule of the invention, which can be chemically-modified, that can be used to modulate the expression of a MAP kinase target gene in a biological system, including, for example, in a cell, tissue, or organism. In another embodiment, the invention features a kit containing more than one siNA molecule of the invention, which can be chemically-modified, that can be used to modulate the expression of more than one MAP kinase target gene in a biological system, including, for example, in a cell, tissue, or organism.

In one embodiment, the invention features a cell containing one or more siNA molecules of the invention, which can be chemically-modified. In another embodiment, the cell containing a siNA molecule of the invention is a mammalian cell. In yet another embodiment, the cell containing a siNA molecule of the invention is a human cell.

In one embodiment, the synthesis of a siNA molecule of the invention, which can be chemically-modified, comprises: (a) synthesis of two complementary strands of the siNA molecule; (b) annealing the two complementary strands together under conditions suitable to obtain a double-stranded siNA molecule. In another embodiment, synthesis of the two complementary strands of the siNA molecule is by solid phase oligonucleotide synthesis. In yet another embodiment, synthesis of the two complementary strands of the siNA molecule is by solid phase tandem oligonucleotide synthesis.

In one embodiment, the invention features a method for synthesizing a siNA duplex molecule comprising: (a) synthesizing a first oligonucleotide sequence strand of the siNA molecule, wherein the first oligonucleotide sequence strand comprises a cleavable linker molecule that can be used as a scaffold for the synthesis of the second oligonucleotide sequence strand of the siNA; (b) synthesizing the second oligonucleotide sequence strand of siNA on the scaffold of the first oligonucleotide sequence strand, wherein the second oligonucleotide sequence strand further comprises a chemical moiety than can be used to purify the siNA duplex; (c) cleaving the linker molecule of (a) under conditions suitable for the two siNA oligonucleotide strands to hybridize and form a stable duplex; and (d) purifying the siNA duplex utilizing the chemical moiety of the second oligonucleotide sequence strand. In one embodiment, cleavage of the linker molecule in (c) above takes place during deprotection of the oligonucleotide, for example, under hydrolysis conditions using an alkylamine base such as methylamine. In one embodiment, the method of synthesis comprises solid phase synthesis on a solid support such as controlled pore glass (CPG) or polystyrene, wherein the first sequence of (a) is synthesized on a cleavable linker, such as a succinyl linker, using the solid support as a scaffold. The cleavable linker in (a) used as a scaffold for synthesizing the second strand can comprise similar reactivity as the solid support derivatized linker, such that cleavage of the solid support derivatized linker and the cleavable linker of (a) takes place concomitantly. In another embodiment, the chemical moiety of (b) that can be used to isolate the attached oligonucleotide sequence comprises a trityl group, for example a dimethoxytrityl group, which can be employed in a trityl-on synthesis strategy as described herein. In yet another embodiment, the chemical moiety, such as a dimethoxytrityl group, is removed during purification, for example, using acidic conditions.

In a further embodiment, the method for siNA synthesis is a solution phase synthesis or hybrid phase synthesis wherein both strands of the siNA duplex are synthesized in tandem using a cleavable linker attached to the first sequence which acts a scaffold for synthesis of the second sequence. Cleavage of the linker under conditions suitable for hybridization of the separate siNA sequence strands results in formation of the double-stranded siNA molecule.

In another embodiment, the invention features a method for synthesizing a siNA duplex molecule comprising: (a) synthesizing one oligonucleotide sequence strand of the siNA molecule, wherein the sequence comprises a cleavable linker molecule that can be used as a scaffold for the synthesis of another oligonucleotide sequence; (b) synthesizing a second oligonucleotide sequence having complementarity to the first sequence strand on the scaffold of (a), wherein the second sequence comprises the other strand of the double-stranded siNA molecule and wherein the second sequence further comprises a chemical moiety than can be used to isolate the attached oligonucleotide sequence; (c) purifying the product of (b) utilizing the chemical moiety of the second oligonucleotide sequence strand under conditions suitable for isolating the full-length sequence comprising both siNA oligonucleotide strands connected by the cleavable linker and under conditions suitable for the two siNA oligonucleotide strands to hybridize and form a stable duplex. In one embodiment, cleavage of the linker molecule in (c) above takes place during deprotection of the oligonucleotide, for example under hydrolysis conditions. In another embodiment, cleavage of the linker molecule in (c) above takes place after deprotection of the oligonucleotide. In another embodiment, the method of synthesis comprises solid phase synthesis on a solid support such as controlled pore glass (CPG) or polystyrene, wherein the first sequence of (a) is synthesized on a cleavable linker, such as a succinyl linker, using the solid support as a scaffold. The cleavable linker in (a) used as a scaffold for synthesizing the second strand can comprise similar reactivity or differing reactivity as the solid support derivatized linker, such that cleavage of the solid support derivatized linker and the cleavable linker of (a) takes place either concomitantly or sequentially. In one embodiment, the chemical moiety of (b) that can be used to isolate the attached oligonucleotide sequence comprises a trityl group, for example a dimethoxytrityl group.

In another embodiment, the invention features a method for making a double-stranded siNA molecule in a single synthetic process comprising: (a) synthesizing an oligonucleotide having a first and a second sequence, wherein the first sequence is complementary to the second sequence, and the first oligonucleotide sequence is linked to the second sequence via a cleavable linker, and wherein a terminal 5′-protecting group, for example, a 5′-O-dimethoxytrityl group (5′-O-DMT) remains on the oligonucleotide having the second sequence; (b) deprotecting the oligonucleotide whereby the deprotection results in the cleavage of the linker joining the two oligonucleotide sequences; and (c) purifying the product of (b) under conditions suitable for isolating the double-stranded siNA molecule, for example using a trityl-on synthesis strategy as described herein.

In another embodiment, the method of synthesis of siNA molecules of the invention comprises the teachings of Scaringe et al., U.S. Pat. Nos. 5,889,136; 6,008,400; and 6,111,086, incorporated by reference herein in their entirety.

In one embodiment, the invention features siNA constructs that mediate RNAi against a MAP kinase, wherein the siNA construct comprises one or more chemical modifications, for example, one or more chemical modifications having any of Formulae I-VII or any combination thereof that increases the nuclease resistance of the siNA construct.

In another embodiment, the invention features a method for generating siNA molecules with increased nuclease resistance comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased nuclease resistance.

In one embodiment, the invention features siNA constructs that mediate RNAi against a MAP kinase, wherein the siNA construct comprises one or more chemical modifications described herein that modulates the binding affinity between the sense and antisense strands of the siNA construct.

In another embodiment, the invention features a method for generating siNA molecules with increased binding affinity between the sense and antisense strands of the siNA molecule comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased binding affinity between the sense and antisense strands of the siNA molecule.

In one embodiment, the invention features siNA constructs that mediate RNAi against a MAP kinase, wherein the siNA construct comprises one or more chemical modifications described herein that modulates the binding affinity between the antisense strand of the siNA construct and a complementary target RNA sequence within a cell.

In one embodiment, the invention features siNA constructs that mediate RNAi against a MAP kinase, wherein the siNA construct comprises one or more chemical modifications described herein that modulates the binding affinity between the antisense strand of the siNA construct and a complementary target DNA sequence within a cell.

In another embodiment, the invention features a method for generating siNA molecules with increased binding affinity between the antisense strand of the siNA molecule and a complementary target RNA sequence comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased binding affinity between the antisense strand of the siNA molecule and a complementary target RNA sequence.

In another embodiment, the invention features a method for generating siNA molecules with increased binding affinity between the antisense strand of the siNA molecule and a complementary target DNA sequence comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased binding affinity between the antisense strand of the siNA molecule and a complementary target DNA sequence.

In one embodiment, the invention features siNA constructs that mediate RNAi against a MAP kinase, wherein the siNA construct comprises one or more chemical modifications described herein that modulate the polymerase activity of a cellular polymerase capable of generating additional endogenous siNA molecules having sequence homology to the chemically-modified siNA construct.

In another embodiment, the invention features a method for generating siNA molecules capable of mediating increased polymerase activity of a cellular polymerase capable of generating additional endogenous siNA molecules having sequence homology to a chemically-modified siNA molecule comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules capable of mediating increased polymerase activity of a cellular polymerase capable of generating additional endogenous siNA molecules having sequence homology to the chemically-modified siNA molecule.

In one embodiment, the invention features chemically-modified siNA constructs that mediate RNAi against a MAP kinase in a cell, wherein the chemical modifications do not significantly effect the interaction of siNA with a target RNA molecule, DNA molecule and/or proteins or other factors that are essential for RNAi in a manner that would decrease the efficacy of RNAi mediated by such siNA constructs.

In another embodiment, the invention features a method for generating siNA molecules with improved RNAi activity against MAP kinase comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved RNAi activity.

In yet another embodiment, the invention features a method for generating siNA molecules with improved RNAi activity against a MAP kinase target RNA comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved RNAi activity against the target RNA.

In yet another embodiment, the invention features a method for generating siNA molecules with improved RNAi activity against a MAP kinase target DNA comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved RNAi activity against the target DNA.

In one embodiment, the invention features siNA constructs that mediate RNAi against a MAP kinase, wherein the siNA construct comprises one or more chemical modifications described herein that modulates the cellular uptake of the siNA construct.

In another embodiment, the invention features a method for generating siNA molecules against MAP kinase with improved cellular uptake comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved cellular uptake.

In one embodiment, the invention features siNA constructs that mediate RNAi against a MAP kinase, wherein the siNA construct comprises one or more chemical modifications described herein that increases the bioavailability of the siNA construct, for example, by attaching polymeric conjugates such as polyethyleneglycol or equivalent conjugates that improve the pharmacokinetics of the siNA construct, or by attaching conjugates that target specific tissue types or cell types in vivo. Non-limiting examples of such conjugates are described in Vargeese et al., U.S. Ser. No. 10/201,394 incorporated by reference herein.

In one embodiment, the invention features a method for generating siNA molecules of the invention with improved bioavailability comprising (a) introducing a conjugate into the structure of a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved bioavailability. Such conjugates can include ligands for cellular receptors, such as peptides derived from naturally occurring protein ligands; protein localization sequences, including cellular ZIP code sequences; antibodies; nucleic acid aptamers; vitamins and other co-factors, such as folate and N-acetylgalactosamine; polymers, such as polyethyleneglycol (PEG); phospholipids; cholesterol; polyamines, such as spermine or spermidine; and others.

In another embodiment, the invention features a method for generating siNA molecules of the invention with improved bioavailability comprising (a) introducing an excipient formulation to a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved bioavailability. Such excipients include polymers such as cyclodextrins, lipids, cationic lipids, polyamines, phospholipids, and others.

In another embodiment, the invention features a method for generating siNA molecules of the invention with improved bioavailability comprising (a) introducing nucleotides having any of Formulae I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved bioavailability.

In another embodiment, polyethylene glycol (PEG) can be covalently attached to siNA compounds of the present invention. The attached PEG can be any molecular weight, preferably from about 2,000 to about 50,000 daltons (Da).

The present invention can be used alone or as a component of a kit having at least one of the reagents necessary to carry out the in vitro or in vivo introduction of RNA to test samples and/or subjects. For example, preferred components of the kit include a siNA molecule of the invention and a vehicle that promotes introduction of the siNA into cells of interest as described herein (e.g., using lipids and other methods of transfection known in the art, see for example Beigelman et al, U.S. Pat. No. 6,395,713). The kit can be used for target validation, such as in determining gene function and/or activity, or in drug optimization, and in drug discovery (see for example Usman et al., U.S. Ser. No. 60/402,996). Such a kit can also include instructions to allow a user of the kit to practice the invention.

The term “short interfering nucleic acid”, “siNA”, “short interfering RNA”, “siRNA”, “short interfering nucleic acid molecule”, “short interfering oligonucleotide molecule”, or “chemically-modified short interfering nucleic acid molecule” as used herein refers to any nucleic acid molecule capable of inhibiting or down regulating gene expression, for example by mediating RNA interference “RNAi” or gene silencing in a sequence-specific manner; see for example Bass, 2001, Nature, 411, 428-429; Elbashir et al., 2001, Nature, 411, 494-498; and Kreutzer et al., International PCT Publication No. WO 00/44895; Zernicka-Goetz et al., International PCT Publication No. WO 01/36646; Fire, International PCT Publication No. WO 99/32619; Plaetinck et al., International PCT Publication No. WO 00/01846; Mello and Fire, International PCT Publication No. WO 01/29058; Deschamps-Depaillette, International PCT Publication No. WO 99/07409; and Li et al., International PCT Publication No. WO 00/44914; Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237; Hutvagner and Zamore, 2002, Science, 297, 2056-60; McManus et al., 2002, RNA, 8, 842-850; Reinhart et al., 2002, Gene & Dev., 16, 1616-1626; and Reinhart & Bartel, 2002, Science, 297, 1831). Non limiting examples of siNA molecules of the invention are shown in FIGS. 4-6, and Tables II, III, and IV herein. For example the siNA can be a double-stranded polynucleotide molecule comprising self-complementary sense and antisense regions, wherein the antisense region comprises nucleotide sequence that is complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof and the sense region having nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof. The siNA can be assembled from two separate oligonucleotides, where one strand is the sense strand and the other is the antisense strand, wherein the antisense and sense strands are self-complementary (i.e. each strand comprises nucleotide sequence that is complementary to nucleotide sequence in the other strand; such as where the antisense strand and sense strand form a duplex or double stranded structure, for example wherein the double stranded region is about 19 base pairs); the antisense strand comprises nucleotide sequence that is complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof and the sense strand comprises nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof. Alternatively, the siNA is assembled from a single oligonucleotide, where the self-complementary sense and antisense regions of the siNA are linked by means of a nucleic acid based or non-nucleic acid-based linker(s). The siNA can be a polynucleotide with a hairpin secondary structure, having self-complementary sense and antisense regions, wherein the antisense region comprises nucleotide sequence that is complementary to nucleotide sequence in a separate target nucleic acid molecule or a portion thereof and the sense region having nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof. The siNA can be a circular single-stranded polynucleotide having two or more loop structures and a stem comprising self-complementary sense and antisense regions, wherein the antisense region comprises nucleotide sequence that is complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof and the sense region having nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof, and wherein the circular polynucleotide can be processed either in vivo or in vitro to generate an active siNA molecule capable of mediating RNAi. The siNA can also comprise a single stranded polynucleotide having nucleotide sequence complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof (for example, where such siNA molecule does not require the presence within the siNA molecule of nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof), wherein the single stranded polynucleotide can further comprise a terminal phosphate group, such as a 5′-phosphate (see for example Martinez et al., 2002, Cell., 110, 563-574 and Schwarz et al., 2002, Molecular Cell, 10, 537-568), or 5′,3′-diphosphate. In certain embodiment, the siNA molecule of the invention comprises separate sense and antisense sequences or regions, wherein the sense and antisense regions are covalently linked by nucleotide or non-nucleotide linkers molecules as is known in the art, or are alternately non-covalently linked by ionic interactions, hydrogen bonding, van der waals interactions, hydrophobic interactions, and/or stacking interactions. In certain embodiments, the siNA molecules of the invention comprise nucleotide sequence that is complementary to nucleotide sequence of a target gene. In another embodiment, the siNA molecule of the invention interacts with nucleotide sequence of a target gene in a manner that causes inhibition of expression of the target gene. As used herein, siNA molecules need not be limited to those molecules containing only RNA, but further encompasses chemically-modified nucleotides and non-nucleotides. In certain embodiments, the short interfering nucleic acid molecules of the invention lack 2′-hydroxy (2′-OH) containing nucleotides. Applicant describes in certain embodiments short interfering nucleic acids that do not require the presence of nucleotides having a 2′-hydroxy group for mediating RNAi and as such, short interfering nucleic acid molecules of the invention optionally do not include any ribonucleotides (e.g., nucleotides having a 2′-OH group). Such siNA molecules that do not require the presence of ribonucleotides within the siNA molecule to support RNAi can however have an attached linker or linkers or other attached or associated groups, moieties, or chains containing one or more nucleotides with 2′-OH groups. Optionally, siNA molecules can comprise ribonucleotides at about 5, 10, 20, 30, 40, or 50% of the nucleotide positions. The modified short interfering nucleic acid molecules of the invention can also be referred to as short interfering modified oligonucleotides “siMON.” As used herein, the term siNA is meant to be equivalent to other terms used to describe nucleic acid molecules that are capable of mediating sequence specific RNAi, for example short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), short hairpin RNA (shRNA), short interfering oligonucleotide, short interfering nucleic acid, short interfering modified oligonucleotide, chemically-modified siRNA, post-transcriptional gene silencing RNA (ptgsRNA), and others. In addition, as used herein, the term RNAi is meant to be equivalent to other terms used to describe sequence specific RNA interference, such as post transcriptional gene silencing, translational inhibition, or epigenetics. For example, siNA molecules of the invention can be used to epigenetically silence genes at both the post-transcriptional level or the pre-transcriptional level. In a non-limiting example, epigenetic regulation of gene expression by siNA molecules of the invention can result from siNA mediated modification of chromatin structure to alter gene expression (see, for example, Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237).

By “modulate” is meant that the expression of the gene, or level of RNA molecule or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits is up regulated or down regulated, such that expression, level, or activity is greater than or less than that observed in the absence of the modulator. For example, the term “modulate” can mean “inhibit,” but the use of the word “modulate” is not limited to this definition.

By “inhibit”, “down-regulate”, or “reduce”, it is meant that the expression of the gene, or level of RNA molecules or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits, is reduced below that observed in the absence of the nucleic acid molecules (e.g., siNA) of the invention. In one embodiment, inhibition, down-regulation or reduction with an siNA molecule is below that level observed in the presence of an inactive or attenuated molecule. In another embodiment, inhibition, down-regulation, or reduction with siNA molecules is below that level observed in the presence of, for example, an siNA molecule with scrambled sequence or with mismatches. In another embodiment, inhibition, down-regulation, or reduction of gene expression with a nucleic acid molecule of the instant invention is greater in the presence of the nucleic acid molecule than in its absence.

By “gene” or “target gene” is meant, a nucleic acid that encodes an RNA, for example, nucleic acid sequences including, but not limited to, structural genes encoding a polypeptide. The target gene can be a gene derived from a cell, an endogenous gene, a transgene, or exogenous genes such as genes of a pathogen, for example a virus, which is present in the cell after infection thereof. The cell containing the target gene can be derived from or contained in any organism, for example a plant, animal, protozoan, virus, bacterium, or fungus. Non-limiting examples of plants include monocots, dicots, or gymnosperms. Non-limiting examples of animals include vertebrates or invertebrates. Non-limiting examples of fungi include molds or yeasts.

By “MAP kinase” is meant, any mitogen activated protein kinase (MAP kinase) polypeptide, protein and/or a polynucleotide encoding a MAP kinase protein (such as polynucleotides referred to by Genbank Accession number in Table I or any other MAP kinase transcript derived from a MAP kinase gene, e.g., c-JUN, ERK1, ERK2, JNK1, JNK2, and/or p38). As used herein, the term “MAP kinase gene” is meant to refer to any polynucleotide included in a group of MAP kinase genes, such as c-JUN, ERK1, ERK2, JNK1, JNK2, and/or p38).

By “MAP kinase protein” is meant, any mitogen activated protein kinase (MAP kinase) peptide or protein or a component thereof, wherein the peptide or protein is encoded by a MAP kinase gene (e.g., c-JUN, ERK1, ERK2, JNK1, JNK2, and/or p38).

By “highly conserved sequence region” is meant a nucleotide sequence of one or more regions in a target gene does not vary significantly from one generation to the other or from one biological system to the other.

By “sense region” is meant a nucleotide sequence of a siNA molecule having complementarity to an antisense region of the siNA molecule. In addition, the sense region of a siNA molecule can comprise a nucleic acid sequence having homology with a target nucleic acid sequence.

By “antisense region” is meant a nucleotide sequence of a siNA molecule having complementarity to a target nucleic acid sequence. In addition, the antisense region of a siNA molecule can optionally comprise a nucleic acid sequence having complementarity to a sense region of the siNA molecule.

By “target nucleic acid” is meant any nucleic acid sequence whose expression or activity is to be modulated. The target nucleic acid can be DNA or RNA.

By “complementarity” is meant that a nucleic acid can form hydrogen bond(s) with another nucleic acid sequence by either traditional Watson-Crick or other non-traditional types. In reference to the nucleic molecules of the present invention, the binding free energy for a nucleic acid molecule with its complementary sequence is sufficient to allow the relevant function of the nucleic acid to proceed, e.g., RNAi activity. Determination of binding free energies for nucleic acid molecules is well known in the art (see, e.g., Turner et al., 1987, CSH Symp. Quant. Biol. LII pp. 123-133; Frier et al., 1986, Proc. Nat. Acad. Sci. USA 83:9373-9377; Turner et al., 1987, J. Am. Chem. Soc. 109:3783-3785). A percent complementarity indicates the percentage of contiguous residues in a nucleic acid molecule that can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%, 90%, and 100% complementary). “Perfectly complementary” means that all the contiguous residues of a nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence.

The siRNA molecules of the invention represent a novel therapeutic approach to treat a variety of pathologic indications or other conditions, including oncology and proliferation related indications and conditions such as multidrug resistant cancers, breast cancer, cancers of the head and neck including various lymphomas such as mantle cell lymphoma, non-Hodgkins lymphoma, adenoma, squamous cell carcinoma, laryngeal carcinoma, cancers of the retina, cancers of the esophagus, multiple myeloma, ovarian cancer, melanoma, colorectal cancer, hepatocellular carcinoma, lung cancer, bladder cancer, pancreatic cancer, prostate cancer, glioblastoma; obesity and insulin resistance (e.g. type I and II diabetes); inflammatory disorders such as asthma, septic shock, rheumatoid arthritis, psoriasis, inflammatory bowl syndrome and any other diseases or conditions that are related to or will respond to the levels of MAP kinase in a cell or tissue, alone or in combination with other therapies. The reduction of MAP kinase expression (specifically MAP kinase gene RNA levels) and thus reduction in the level of the respective protein relieves, to some extent, the symptoms of the disease or condition.

In one embodiment of the present invention, each sequence of a siNA molecule of the invention is independently about 18 to about 24 nucleotides in length, in specific embodiments about 18, 19, 20, 21, 22, 23, or 24 nucleotides in length. In another embodiment, the siNA duplexes of the invention independently comprise about 17 to about 23 base pairs (e.g., about 17, 18, 19, 20, 21, 22 or 23). In yet another embodiment, siNA molecules of the invention comprising hairpin or circular structures are about 35 to about 55 (e.g., about 35, 40, 45, 50 or 55) nucleotides in length, or about 38 to about 44 (e.g., 38, 39, 40, 41, 42, 43 or 44) nucleotides in length and comprising about 16 to about 22 (e.g., about 16, 17, 18, 19, 20, 21 or 22) base pairs. Exemplary siNA molecules of the invention are shown in Table II. Exemplary synthetic siNA molecules of the invention are shown in Tables III and IV and/or FIGS. 4-5.

As used herein “cell” is used in its usual biological sense, and does not refer to an entire multicellular organism, e.g., specifically does not refer to a human. The cell can be present in an organism, e.g., birds, plants and mammals such as humans, cows, sheep, apes, monkeys, swine, dogs, and cats. The cell can be prokaryotic (e.g., bacterial cell) or eukaryotic (e.g., mammalian or plant cell). The cell can be of somatic or germ line origin, totipotent or pluripotent, dividing or non-dividing. The cell can also be derived from or can comprise a gamete or embryo, a stem cell, or a fully differentiated cell.

The siNA molecules of the invention are added directly, or can be complexed with cationic lipids, packaged within liposomes, or otherwise delivered to target cells or tissues. The nucleic acid or nucleic acid complexes can be locally administered to relevant tissues ex vivo, or in vivo through injection, infusion pump or stent, with or without their incorporation in biopolymers. In particular embodiments, the nucleic acid molecules of the invention comprise sequences shown in Tables II-III and/or FIGS. 4-5. Examples of such nucleic acid molecules consist essentially of sequences defined in these tables and figures. Furthermore, the chemically modified constructs described in Table IV can be applied to any siNA sequence of the invention.

In another aspect, the invention provides mammalian cells containing one or more siNA molecules of this invention. The one or more siNA molecules can independently be targeted to the same or different sites.

By “RNA” is meant a molecule comprising at least one ribonucleotide residue. By “ribonucleotide” is meant a nucleotide with a hydroxyl group at the 2′ position of a β-D-ribo-furanose moiety. The terms include double-stranded RNA, single-stranded RNA, isolated RNA such as partially purified RNA, essentially pure RNA, synthetic RNA, recombinantly produced RNA, as well as altered RNA that differs from naturally occurring RNA by the addition, deletion, substitution and/or alteration of one or more nucleotides. Such alterations can include addition of non-nucleotide material, such as to the end(s) of the siNA or internally, for example at one or more nucleotides of the RNA. Nucleotides in the RNA molecules of the instant invention can also comprise non-standard nucleotides, such as non-naturally occurring nucleotides or chemically synthesized nucleotides or deoxynucleotides. These altered RNAs can be referred to as analogs or analogs of naturally-occurring RNA.

By “subject” is meant an organism, which is a donor or recipient of explanted cells or the cells themselves. “Subject” also refers to an organism to which the nucleic acid molecules of the invention can be administered. A subject can be a mammal or mammalian cells, including a human or human cells.

The term “phosphorothioate” as used herein refers to an internucleotide linkage having Formula I, wherein Z and/or W comprise a sulfur atom. Hence, the term phosphorothioate refers to both phosphorothioate and phosphorodithioate internucleotide linkages.

The term “universal base” as used herein refers to nucleotide base analogs that form base pairs with each of the natural DNA/RNA bases with little discrimination between them. Non-limiting examples of universal bases include C-phenyl, C-naphthyl and other aromatic derivatives, inosine, azole carboxamides, and nitroazole derivatives such as 3-nitropyrrole, 4-nitroindole, 5-nitroindole, and 6-nitroindole as known in the art (see for example Loakes, 2001, Nucleic Acids Research, 29, 2437-2447).

The term “acyclic nucleotide” as used herein refers to any nucleotide having an acyclic ribose sugar, for example where any of the ribose carbons (C1, C2, C3, C4, or C5), are independently or in combination absent from the nucleotide.

The nucleic acid molecules of the instant invention, individually, or in combination or in conjunction with other drugs, can be used to treat diseases or conditions discussed herein (e.g., cancers and other proliferative conditions). For example, to treat a particular disease or condition, the siNA molecules can be administered to a subject or can be administered to other appropriate cells evident to those skilled in the art, individually or in combination with one or more drugs under conditions suitable for the treatment.

In a further embodiment, the siNA molecules can be used in combination with other known treatments to treat conditions or diseases discussed above. For example, the described molecules could be used in combination with one or more known therapeutic agents to treat a disease or condition. Non-limiting examples of other therapeutic agents that can be readily combined with a siNA molecule of the invention are enzymatic nucleic acid molecules, allosteric nucleic acid molecules, antisense, decoy, or aptamer nucleic acid molecules, antibodies such as monoclonal antibodies, small molecules, and other organic and/or inorganic compounds including metals, salts and ions.

In one embodiment, the invention features an expression vector comprising a nucleic acid sequence encoding at least one siNA molecule of the invention, in a manner which allows expression of the siNA molecule. For example, the vector can contain sequence(s) encoding both strands of a siNA molecule comprising a duplex. The vector can also contain sequence(s) encoding a single nucleic acid molecule that is self-complementary and thus forms a siNA molecule. Non-limiting examples of such expression vectors are described in Paul et al., 2002, Nature Biotechnology, 19, 505; Miyagishi and Taira, 2002, Nature Biotechnology, 19, 497; Lee et al., 2002, Nature Biotechnology, 19, 500; and Novina et al., 2002, Nature Medicine, advance online publication doi:10.1038/nm725.

In another embodiment, the invention features a mammalian cell, for example, a human cell, including an expression vector of the invention.

In yet another embodiment, the expression vector of the invention comprises a sequence for a siNA molecule having complementarity to a RNA molecule referred to by a Genbank Accession numbers, for example Genbank Accession Nos. shown in Table I.

In one embodiment, an expression vector of the invention comprises a nucleic acid sequence encoding two or more siNA molecules, which can be the same or different.

In another aspect of the invention, siNA molecules that interact with target RNA molecules and down-regulate gene encoding target RNA molecules (for example target RNA molecules referred to by Genbank Accession numbers herein) are expressed from transcription units inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. siNA expressing viral vectors can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. The recombinant vectors capable of expressing the siNA molecules can be delivered as described herein, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of siNA molecules. Such vectors can be repeatedly administered as necessary. Once expressed, the siNA molecules bind and down-regulate gene function or expression via RNA interference (RNAi). Delivery of siNA expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell.

By “vectors” is meant any nucleic acid- and/or viral-based technique used to deliver a desired nucleic acid.

Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a non-limiting example of a scheme for the synthesis of siNA molecules. The complementary siNA sequence strands, strand 1 and strand 2, are synthesized in tandem and are connected by a cleavable linkage, such as a nucleotide succinate or abasic succinate, which can be the same or different from the cleavable linker used for solid phase synthesis on a solid support. The synthesis can be either solid phase or solution phase, in the example shown, the synthesis is a solid phase synthesis. The synthesis is performed such that a protecting group, such as a dimethoxytrityl group, remains intact on the terminal nucleotide of the tandem oligonucleotide. Upon cleavage and deprotection of the oligonucleotide, the two siNA strands spontaneously hybridize to form a siNA duplex, which allows the purification of the duplex by utilizing the properties of the terminal protecting group, for example by applying a trityl on purification method wherein only duplexes/oligonucleotides with the terminal protecting group are isolated.

FIG. 2 shows a MALDI-TOF mass spectrum of a purified siNA duplex synthesized by a method of the invention. The two peaks shown correspond to the predicted mass of the separate siNA sequence strands. This result demonstrates that the siNA duplex generated from tandem synthesis can be purified as a single entity using a simple trityl-on purification methodology.

FIG. 3 shows a non-limiting proposed mechanistic representation of target RNA degradation involved in RNAi. Double-stranded RNA (dsRNA), which is generated by RNA-dependent RNA polymerase (RdRP) from foreign single-stranded RNA, for example viral, transposon, or other exogenous RNA, activates the DICER enzyme that in turn generates siNA duplexes. Alternately, synthetic or expressed siNA can be introduced directly into a cell by appropriate means. An active siNA complex forms which recognizes a target RNA, resulting in degradation of the target RNA by the RISC endonuclease complex or in the synthesis of additional RNA by RNA-dependent RNA polymerase (RdRP), which can activate DICER and result in additional siNA molecules, thereby amplifying the RNAi response.

FIG. 4A-F shows non-limiting examples of chemically-modified siNA constructs of the present invention. In the figure, N stands for any nucleotide (adenosine, guanosine, cytosine, uridine, or optionally thymidine, for example thymidine can be substituted in the overhanging regions designated by parenthesis (N N). Various modifications are shown for the sense and antisense strands of the siNA constructs.

FIG. 4A: The sense strand comprises 21 nucleotides wherein the two terminal 3′-nucleotides are optionally base paired and wherein all nucleotides present are ribonucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand comprises 21 nucleotides, optionally having a 3′-terminal glyceryl moiety and wherein the two terminal 3′-nucleotides are optionally complementary to the target RNA sequence, and wherein all nucleotides present are ribonucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as “s” connects the (N N) nucleotides in the antisense strand.

FIG. 4B: The sense strand comprises 21 nucleotides wherein the two terminal 3′-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides and all purine nucleotides that may be present are 2′-O-methyl modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand comprises 21 nucleotides, optionally having a 3′-terminal glyceryl moiety and wherein the two terminal 3′-nucleotides are optionally complementary to the target RNA sequence, and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides and all purine nucleotides that may be present are 2′-O-methyl modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as “s” connects the (N N) nucleotides in the sense and antisense strand.

FIG. 4C: The sense strand comprises 21 nucleotides having 5′- and 3′-terminal cap moieties wherein the two terminal 3′-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2′-O-methyl or 2′-deoxy-2′-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand comprises 21 nucleotides, optionally having a 3′-terminal glyceryl moiety and wherein the two terminal 3′-nucleotides are optionally complementary to the target RNA sequence, and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as “s” connects the (N N) nucleotides in the antisense strand.

FIG. 4D: The sense strand comprises 21 nucleotides having 5′- and 3′-terminal cap moieties wherein the two terminal 3′-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein and wherein and all purine nucleotides that may be present are 2′-deoxy nucleotides. The antisense strand comprises 21 nucleotides, optionally having a 3′-terminal glyceryl moiety and wherein the two terminal 3′-nucleotides are optionally complementary to the target RNA sequence, and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides and all purine nucleotides that may be present are 2′-O-methyl modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as “s” connects the (N N) nucleotides in the antisense strand.

FIG. 4E: The sense strand comprises 21 nucleotides having 5′- and 3′-terminal cap moieties wherein the two terminal 3′-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand comprises 21 nucleotides, optionally having a 3′-terminal glyceryl moiety and wherein the two terminal 3′-nucleotides are optionally complementary to the target RNA sequence, and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides and all purine nucleotides that may be present are 2′-O-methyl modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as “s” connects the (N N) nucleotides in the antisense strand.

FIG. 4F: The sense strand comprises 21 nucleotides having 5′- and 3′-terminal cap moieties wherein the two terminal 3′-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein and wherein and all purine nucleotides that may be present are 2′-deoxy nucleotides. The antisense strand comprises 21 nucleotides, optionally having a 3′-terminal glyceryl moiety and wherein the two terminal 3′-nucleotides are optionally complementary to the target RNA sequence, and wherein all pyrimidine nucleotides that may be present are 2′-deoxy-2′-fluoro modified nucleotides and all purine nucleotides that may be present are 2′-deoxy nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as “s” connects the (N N) nucleotides in the antisense strand. The antisense strand of constructs A-F comprise sequence complementary to any target nucleic acid sequence of the invention. Furthermore, when a glyceryl moiety (L) is present at the 3′-end of the antisense strand for any construct shown in FIG. 4 A-F, the modified internucleotide linkage is optional.

FIG. 5A-F shows non-limiting examples of specific chemically-modified siNA sequences of the invention. A-F applies the chemical modifications described in FIG. 4A-F to a c-JUN siNA sequence. Such chemical modifications can be applied to any sequence herein, such as any MAP kinase sequence.

FIG. 6 shows non-limiting examples of different siNA constructs of the invention. The examples shown (constructs 1, 2, and 3) have 19 representative base pairs; however, different embodiments of the invention include any number of base pairs described herein. Bracketed regions represent nucleotide overhangs, for example comprising about 1, 2, 3, or 4 nucleotides in length, preferably about 2 nucleotides. Constructs 1 and 2 can be used independently for RNAi activity. Construct 2 can comprise a polynucleotide or non-nucleotide linker, which can optionally be designed as a biodegradable linker. In one embodiment, the loop structure shown in construct 2 can comprise a biodegradable linker that results in the formation of construct 1 in vivo and/or in vitro. In another example, construct 3 can be used to generate construct 2 under the same principle wherein a linker is used to generate the active siNA construct 2 in vivo and/or in vitro, which can optionally utilize another biodegradable linker to generate the active siNA construct 1 in vivo and/or in vitro. As such, the stability and/or activity of the siNA constructs can be modulated based on the design of the siNA construct for use in vivo or in vitro and/or in vitro.

FIG. 7A-C is a diagrammatic representation of a scheme utilized in generating an expression cassette to generate siNA hairpin constructs.

FIG. 7A: A DNA oligomer is synthesized with a 5′-restriction site (R1) sequence followed by a region having sequence identical (sense region of siNA) to a predetermined MAP kinase target sequence, wherein the sense region comprises, for example, about 19, 20, 21, or 22 nucleotides (N) in length, which is followed by a loop sequence of defined sequence (X), comprising, for example, about 3 to about 10 nucleotides.

FIG. 7B: The synthetic construct is then extended by DNA polymerase to generate a hairpin structure having self-complementary sequence that will result in a siNA transcript having specificity for a MAP kinase target sequence and having self-complementary sense and antisense regions.

FIG. 7C: The construct is heated (for example to about 95° C.) to linearize the sequence, thus allowing extension of a complementary second DNA strand using a primer to the 3′-restriction sequence of the first strand. The double-stranded DNA is then inserted into an appropriate vector for expression in cells. The construct can be designed such that a 3′-terminal nucleotide overhang results from the transcription, for example by engineering restriction sites and/or utilizing a poly-U termination region as described in Paul et al., 2002, Nature Biotechnology, 29, 505-508.

FIG. 8A-C is a diagrammatic representation of a scheme utilized in generating an expression cassette to generate double-stranded siNA constructs.

FIG. 8A: A DNA oligomer is synthesized with a 5′-restriction (R1) site sequence followed by a region having sequence identical (sense region of siNA) to a predetermined MAP kinase target sequence, wherein the sense region comprises, for example, about 19, 20, 21, or 22 nucleotides (N) in length, and which is followed by a 3′-restriction site (R2) which is adjacent to a loop sequence of defined sequence (X).

FIG. 8B: The synthetic construct is then extended by DNA polymerase to generate a hairpin structure having self-complementary sequence.

FIG. 8C: The construct is processed by restriction enzymes specific to R1 and R2 to generate a double-stranded DNA which is then inserted into an appropriate vector for expression in cells. The transcription cassette is designed such that a U6 promoter region flanks each side of the dsDNA which generates the separate sense and antisense strands of the siNA. Poly T termination sequences can be added to the constructs to generate U overhangs in the resulting transcript.

FIG. 9A-E is a diagrammatic representation of a method used to determine target sites for siNA mediated RNAi within a particular target nucleic acid sequence, such as messenger RNA.

FIG. 9A: A pool of siNA oligonucleotides are synthesized wherein the antisense region of the siNA constructs has complementarity to target sites across the target nucleic acid sequence, and wherein the sense region comprises sequence complementary to the antisense region of the siNA.

FIGS. 9B&C: (FIG. 9B) The sequences are pooled and are inserted into vectors such that (FIG. 9C) transfection of a vector into cells results in the expression of the siNA.

FIG. 9D: Cells are sorted based on phenotypic change that is associated with modulation of the target nucleic acid sequence.

FIG. 9E: The siNA is isolated from the sorted cells and is sequenced to identify efficacious target sites within the target nucleic acid sequence.

FIG. 10 shows non-limiting examples of different stabilization chemistries (1-10) that can be used, for example, to stabilize the 3′-end of siNA sequences of the invention, including (1) [3-3′]-inverted deoxyribose; (2) deoxyribonucleotide; (3) [5′-3′]-3′-deoxyribonucleotide; (4) [5′-3′]-ribonucleotide; (5) [5′-3′]-3′-O-methyl ribonucleotide; (6) 3′-glyceryl; (7) [3′-5′]-3′-deoxyribonucleotide; (8) [3′-3′]-deoxyribonucleotide; (9) [5′-2′]-deoxyribonucleotide; and (10) [5-3′]-dideoxyribonucleotide. In addition to modified and unmodified backbone chemistries indicated in the figure, these chemistries can be combined with different backbone modifications as described herein, for example, backbone modifications having Formula I. In addition, the 2′-deoxy nucleotide shown 5′ to the terminal modifications shown can be another modified or unmodified nucleotide or non-nucleotide described herein, for example modifications having any of Formulae I-VII or any combination thereof.

FIG. 11 shows a non-limiting example of a strategy used to identify chemically modified siNA constructs of the invention that are nuclease resistance while preserving the ability to mediate RNAi activity. Chemical modifications are introduced into the siNA construct based on educated design parameters (e.g. introducing 2′-modifications, base modifications, backbone modifications, terminal cap modifications etc). The modified construct in tested in an appropriate system (e.g. human serum for nuclease resistance, shown, or an animal model for PK/delivery parameters). In parallel, the siNA construct is tested for RNAi activity, for example in a cell culture system such as a luciferase reporter assay). Lead siNA constructs are then identified which possess a particular characteristic while maintaining RNAi activity, and can be further modified and assayed once again. This same approach can be used to identify siNA-conjugate molecules with improved pharmacokinetic profiles, delivery, and RNAi activity.

FIG. 12 shows a non-limiting example of reduction of p38 mRNA in A549 cells mediated by siNAs that target p38 mRNA. A549 cells were transfected with 0.25 ug/well of lipid complexed with 25 nM siNA. A screen of siNA constructs comprising ribonucleotides and 3′-terminal dithymidine caps was compared to untreated cells, scrambled siNA control constructs (Scram1 and Scram2), and cells transfected with lipid alone (transfection control). As shown in the figure, the siNA constructs significantly reduce p38 RNA expression.

FIG. 13 shows a non-limiting example of reduction of JNK1 mRNA in A549 cells mediated by siNAs that target JNK1 mRNA. A549 cells were transfected with 0.25 ug/well of lipid complexed with 25 nM siNA. A screen of siNA constructs comprising ribonucleotides and 3′-terminal dithymidine caps was compared to untreated cells, scrambled siNA control constructs (Scram1 and Scram2), and cells transfected with lipid alone (transfection control). As shown in the figure, the siNA constructs significantly reduce JNK1 RNA expression.

DETAILED DESCRIPTION OF THE INVENTION Mechanism of Action of Nucleic Acid Molecules of the Invention

The discussion that follows discusses the proposed mechanism of RNA interference mediated by short interfering RNA as is presently known, and is not meant to be limiting and is not an admission of prior art. Applicant demonstrates herein that chemically-modified short interfering nucleic acids possess similar or improved capacity to mediate RNAi as do siRNA molecules and are expected to possess improved stability and activity in vivo; therefore, this discussion is not meant to be limited to siRNA only and can be applied to siNA as a whole. By “improved capacity to mediate RNAi” or “improved RNAi activity” is meant to include RNAi activity measured in vitro and/or in vivo where the RNAi activity is a reflection of both the ability of the siNA to mediate RNAi and the stability of the siNAs of the invention. In this invention, the product of these activities can be increased in vitro and/or in vivo compared to an all RNA siRNA or a siNA containing a plurality of ribonucleotides. In some cases, the activity or stability of the siNA molecule can be decreased (i.e., less than ten-fold), but the overall activity of the siNA molecule is enhanced in vitro and/or in vivo.

RNA interference refers to the process of sequence specific post-transcriptional gene silencing in animals mediated by short interfering RNAs (siRNAs) (Fire et al., 1998, Nature, 391, 806). The corresponding process in plants is commonly referred to as post-transcriptional gene silencing or RNA silencing and is also referred to as quelling in fungi. The process of post-transcriptional gene silencing is thought to be an evolutionarily-conserved cellular defense mechanism used to prevent the expression of foreign genes which is commonly shared by diverse flora and phyla (Fire et al., 1999, Trends Genet., 15, 358). Such protection from foreign gene expression may have evolved in response to the production of double-stranded RNAs (dsRNAs) derived from viral infection or the random integration of transposon elements into a host genome via a cellular response that specifically destroys homologous single-stranded RNA or viral genomic RNA. The presence of dsRNA in cells triggers the RNAi response though a mechanism that has yet to be fully characterized. This mechanism appears to be different from the interferon response that results from dsRNA-mediated activation of protein kinase PKR and 2′,5′-oligoadenylate synthetase resulting in non-specific cleavage of mRNA by ribonuclease L.

The presence of long dsRNAs in cells stimulates the activity of a ribonuclease III enzyme referred to as Dicer. Dicer is involved in the processing of the dsRNA into short pieces of dsRNA known as short interfering RNAs (siRNAs) (Berstein et al., 2001, Nature, 409, 363). Short interfering RNAs derived from Dicer activity are typically about 21 to about 23 nucleotides in length and comprise about 19 base pair duplexes. Dicer has also been implicated in the excision of 21- and 22-nucleotide small temporal RNAs (stRNAs) from precursor RNA of conserved structure that are implicated in translational control (Hutvagner et al., 2001, Science, 293, 834). The RNAi response also features an endonuclease complex containing a siRNA, commonly referred to as an RNA-induced silencing complex (RISC), which mediates cleavage of single-stranded RNA having sequence homologous to the siRNA. Cleavage of the target RNA takes place in the middle of the region complementary to the guide sequence of the siRNA duplex (Elbashir et al., 2001, Genes Dev., 15, 188). In addition, RNA interference can also involve small RNA (e.g., micro-RNA or miRNA) mediated gene silencing, presumably though cellular mechanisms that regulate chromatin structure and thereby prevent transcription of target gene sequences (see for example Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237). As such, siNA molecules of the invention can be used to mediate gene silencing via interaction with RNA transcripts or alternately by interaction with particular gene sequences, wherein such interaction results in gene silencing either at the transcriptional level or post-transcriptional level.

RNAi has been studied in a variety of systems. Fire et al., 1998, Nature, 391, 806, were the first to observe RNAi in C. elegans. Wianny and Goetz, 1999, Nature Cell Biol., 2, 70, describe RNAi mediated by dsRNA in mouse embryos. Hammond et al., 2000, Nature, 404, 293, describe RNAi in Drosophila cells transfected with dsRNA. Elbashir et al., 2001, Nature, 411, 494, describe RNAi induced by introduction of duplexes of synthetic 21-nucleotide RNAs in cultured mammalian cells including human embryonic kidney and HeLa cells. Recent work in Drosophila embryonic lysates has revealed certain requirements for siRNA length, structure, chemical composition, and sequence that are essential to mediate efficient RNAi activity. These studies have shown that 21 nucleotide siRNA duplexes are most active when containing two 2-nucleotide 3′-terminal nucleotide overhangs. Furthermore, substitution of one or both siRNA strands with 2′-deoxy or 2′-O-methyl nucleotides abolishes RNAi activity, whereas substitution of 3′-terminal siRNA nucleotides with deoxy nucleotides was shown to be tolerated. Mismatch sequences in the center of the siRNA duplex were also shown to abolish RNAi activity. In addition, these studies also indicate that the position of the cleavage site in the target RNA is defined by the 5′-end of the siRNA guide sequence rather than the 3′-end (Elbashir et al., 2001, EMBO J., 20, 6877). Other studies have indicated that a 5′-phosphate on the target-complementary strand of a siRNA duplex is required for siRNA activity and that ATP is utilized to maintain the 5′-phosphate moiety on the siRNA (Nykanen et al., 2001, Cell, 107, 309); however, siRNA molecules lacking a 5′-phosphate are active when introduced exogenously, suggesting that 5′-phosphorylation of siRNA constructs may occur in vivo.

Synthesis of Nucleic Acid Molecules

Synthesis of nucleic acids greater than 100 nucleotides in length is difficult using automated methods, and the therapeutic cost of such molecules is prohibitive. In this invention, small nucleic acid motifs (“small” refers to nucleic acid motifs no more than 100 nucleotides in length, preferably no more than 80 nucleotides in length, and most preferably no more than 50 nucleotides in length; e.g., individual siNA oligonucleotide sequences or siNA sequences synthesized in tandem) are preferably used for exogenous delivery. The simple structure of these molecules increases the ability of the nucleic acid to invade targeted regions of protein and/or RNA structure. Exemplary molecules of the instant invention are chemically synthesized, and others can similarly be synthesized.

Oligonucleotides (e.g., certain modified oligonucleotides or portions of oligonucleotides lacking ribonucleotides) are synthesized using protocols known in the art, for example as described in Caruthers et al., 1992, Methods in Enzymology 211, 3-19, Thompson et al., International PCT Publication No. WO 99/54459, Wincott et al., 1995, Nucleic Acids Res. 23, 2677-2684, Wincott et al., 1997, Methods Mol. Bio., 74, 59, Brennan et al., 1998, Biotechnol Bioeng., 61, 33-45, and Brennan, U.S. Pat. No. 6,001,311. All of these references are incorporated herein by reference. The synthesis of oligonucleotides makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5′-end, and phosphoramidites at the 3′-end. In a non-limiting example, small scale syntheses are conducted on a 394 Applied Biosystems, Inc. synthesizer using a 0.2 μmol scale protocol with a 2.5 minute coupling step for 2′-O-methylated nucleotides and a 45 second coupling step for 2′-deoxy nucleotides or 2′-deoxy-2′-fluoro nucleotides. Table V outlines the amounts and the contact times of the reagents used in the synthesis cycle. Alternatively, syntheses at the 0.2 μmol scale can be performed on a 96-well plate synthesizer, such as the instrument produced by Protogene (Palo Alto, Calif.) with minimal modification to the cycle. A 33-fold excess (60 μL of 0.11 M=6.6 μmol) of 2′-O-methyl phosphoramidite and a 105-fold excess of S-ethyl tetrazole (60 μL of 0.25 M=15 μmol) can be used in each coupling cycle of 2′-O-methyl residues relative to polymer-bound 5′-hydroxyl. A 22-fold excess (40 μL of 0.11 M=4.4 μmol) of deoxy phosphoramidite and a 70-fold excess of S-ethyl tetrazole (40 μL of 0.25 M=10 μmol) can be used in each coupling cycle of deoxy residues relative to polymer-bound 5′-hydroxyl. Average coupling yields on the 394 Applied Biosystems, Inc. synthesizer, determined by colorimetric quantitation of the trityl fractions, are typically 97.5-99%. Other oligonucleotide synthesis reagents for the 394 Applied Biosystems, Inc. synthesizer include the following: detritylation solution is 3% TCA in methylene chloride (ABI); capping is performed with 16% N-methyl imidazole in THF (ABI) and 10% acetic anhydride/10% 2,6-lutidine in THF (ABI); and oxidation solution is 16.9 mM 12, 49 mM pyridine, 9% water in THF (PERSEPTIVE™). Burdick & Jackson Synthesis Grade acetonitrile is used directly from the reagent bottle. S-Ethyltetrazole solution (0.25 M in acetonitrile) is made up from the solid obtained from American International Chemical, Inc. Alternately, for the introduction of phosphorothioate linkages, Beaucage reagent (3H-1,2-Benzodithiol-3-one 1,1-dioxide, 0.05 M in acetonitrile) is used.

Deprotection of the DNA-based oligonucleotides is performed as follows: the polymer-bound trityl-on oligoribonucleotide is transferred to a 4 mL glass screw top vial and suspended in a solution of 40% aqueous methylamine (1 mL) at 65° C. for 10 minutes. After cooling to −20° C., the supernatant is removed from the polymer support. The support is washed three times with 1.0 mL of EtOH:MeCN:H₂O/3:1:1, vortexed and the supernatant is then added to the first supernatant. The combined supernatants, containing the oligoribonucleotide, are dried to a white powder.

The method of synthesis used for RNA including certain siNA molecules of the invention follows the procedure as described in Usman et al., 1987, J. Am. Chem. Soc., 109, 7845; Scaringe et al., 1990, Nucleic Acids Res., 18, 5433; and Wincott et al., 1995, Nucleic Acids Res. 23, 2677-2684 Wincott et al., 1997, Methods Mol. Bio., 74, 59, and makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5′-end, and phosphoramidites at the 3′-end. In a non-limiting example, small scale syntheses are conducted on a 394 Applied Biosystems, Inc. synthesizer using a 0.2 μmol scale protocol with a 7.5 minute coupling step for alkylsilyl protected nucleotides and a 2.5 minute coupling step for 2′-O-methylated nucleotides. Table V outlines the amounts and the contact times of the reagents used in the synthesis cycle. Alternatively, syntheses at the 0.2 μmol scale can be done on a 96-well plate synthesizer, such as the instrument produced by Protogene (Palo Alto, Calif.) with minimal modification to the cycle. A 33-fold excess (60 μL of 0.11 M=6.6 μmol) of 2′-O-methyl phosphoramidite and a 75-fold excess of S-ethyl tetrazole (60 μL of 0.25 M=15 μmol) can be used in each coupling cycle of 2′-O-methyl residues relative to polymer-bound 5′-hydroxyl. A 66-fold excess (120 μL of 0.11 M=13.2 μmol) of alkylsilyl (ribo) protected phosphoramidite and a 150-fold excess of S-ethyl tetrazole (120 μL of 0.25 M=30 μmol) can be used in each coupling cycle of ribo residues relative to polymer-bound 5′-hydroxyl. Average coupling yields on the 394 Applied Biosystems, Inc. synthesizer, determined by colorimetric quantitation of the trityl fractions, are typically 97.5-99%. Other oligonucleotide synthesis reagents for the 394 Applied Biosystems, Inc. synthesizer include the following: detritylation solution is 3% TCA in methylene chloride (ABI); capping is performed with 16% N-methyl imidazole in THF (ABI) and 10% acetic anhydride/10% 2,6-lutidine in THF (ABI); oxidation solution is 16.9 mM 12, 49 mM pyridine, 9% water in THF (PERSEPTIVE™). Burdick & Jackson Synthesis Grade acetonitrile is used directly from the reagent bottle. S-Ethyltetrazole solution (0.25 M in acetonitrile) is made up from the solid obtained from American International Chemical, Inc. Alternately, for the introduction of phosphorothioate linkages, Beaucage reagent (3H-1,2-Benzodithiol-3-one 1,1-dioxide 0.05 M in acetonitrile) is used.

Deprotection of the RNA is performed using either a two-pot or one-pot protocol. For the two-pot protocol, the polymer-bound trityl-on oligoribonucleotide is transferred to a 4 mL glass screw top vial and suspended in a solution of 40% aq. methylamine (1 mL) at 65° C. for 10 minutes. After cooling to −20° C., the supernatant is removed from the polymer support. The support is washed three times with 1.0 mL of EtOH:MeCN:H₂O/3:1:1, vortexed and the supernatant is then added to the first supernatant. The combined supernatants, containing the oligoribonucleotide, are dried to a white powder. The base deprotected oligoribonucleotide is resuspended in anhydrous TEA/HF/NMP solution (300 μL of a solution of 1.5 mL N-methylpyrrolidinone, 750 μL TEA and 1 mL TEA.3HF to provide a 1.4 M HF concentration) and heated to 65° C. After 1.5 hours, the oligomer is quenched with 1.5 M NH₄HCO₃.

Alternatively, for the one-pot protocol, the polymer-bound trityl-on oligoribonucleotide is transferred to a 4 mL glass screw top vial and suspended in a solution of 33% ethanolic methylamine/DMSO: 1/1 (0.8 mL) at 65° C. for 15 minutes. The vial is brought to room temperature. TEA.3HF (0.1 mL) is added and the vial is heated at 65° C. for 15 minutes. The sample is cooled at −20° C. and then quenched with 1.5 M NH₄HCO₃.

For purification of the trityl-on oligomers, the quenched NH₄.HCO₃ solution is loaded onto a C-18 containing cartridge that had been prewashed with acetonitrile followed by 50 mM TEAA. After washing the loaded cartridge with water, the RNA is detritylated with 0.5% TFA for 13 minutes. The cartridge is then washed again with water, salt exchanged with 1 M NaCl and washed with water again. The oligonucleotide is then eluted with 30% acetonitrile.

The average stepwise coupling yields are typically >98% (Wincott et al., 1995 Nucleic Acids Res. 23, 2677-2684). Those of ordinary skill in the art will recognize that the scale of synthesis can be adapted to be larger or smaller than the example described above including but not limited to 96-well format.

Alternatively, the nucleic acid molecules of the present invention can be synthesized separately and joined together post-synthetically, for example, by ligation (Moore et al., 1992, Science 256, 9923; Draper et al., International PCT publication No. WO 93/23569; Shabarova et al., 1991, Nucleic Acids Research 19, 4247; Bellon et al., 1997, Nucleosides & Nucleotides, 16, 951; Bellon et al., 1997, Bioconjugate Chem. 8, 204), or by hybridization following synthesis and/or deprotection.

The siNA molecules of the invention can also be synthesized via a tandem synthesis methodology as described in Example 1 herein, wherein both siNA strands are synthesized as a single contiguous oligonucleotide fragment or strand separated by a cleavable linker which is subsequently cleaved to provide separate siNA fragments or strands that hybridize and permit purification of the siNA duplex. The linker can be a polynucleotide linker or a non-nucleotide linker. The tandem synthesis of siNA as described herein can be readily adapted to both multiwell/multiplate synthesis platforms such as 96 well or similarly larger multi-well platforms. The tandem synthesis of siNA as described herein can also be readily adapted to large scale synthesis platforms employing batch reactors, synthesis columns and the like.

A siNA molecule can also be assembled from two distinct nucleic acid strands or fragments wherein one fragment includes the sense region and the second fragment includes the antisense region of the RNA molecule.

The nucleic acid molecules of the present invention can be modified extensively to enhance stability by modification with nuclease resistant groups, for example, 2′-amino, 2′-C-allyl, 2′-fluoro, 2′-O-methyl, 2′-H (for a review see Usman and Cedergren, 1992, TIBS 17, 34; Usman et al., 1994, Nucleic Acids Symp. Ser. 31, 163). siNA constructs can be purified by gel electrophoresis using general methods or can be purified by high pressure liquid chromatography (HPLC; see Wincott et al., supra, the totality of which is hereby incorporated herein by reference) and re-suspended in water.

In another aspect of the invention, siNA molecules of the invention are expressed from transcription units inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. siNA expressing viral vectors can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. The recombinant vectors capable of expressing the siNA molecules can be delivered as described herein, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of siNA molecules.

Optimizing Activity of the Nucleic Acid Molecule of the Invention.

Chemically synthesizing nucleic acid molecules with modifications (base, sugar and/or phosphate) can prevent their degradation by serum ribonucleases, which can increase their potency (see e.g., Eckstein et al., International Publication No. WO 92/07065; Perrault et al., 1990 Nature 344, 565; Pieken et al., 1991, Science 253, 314; Usman and Cedergren, 1992, Trends in Biochem. Sci. 17, 334; Usman et al., International Publication No. WO 93/15187; and Rossi et al., International Publication No. WO 91/03162; Sproat, U.S. Pat. No. 5,334,711; Gold et al., U.S. Pat. No. 6,300,074; and Burgin et al., supra; all of which are incorporated by reference herein). All of the above references describe various chemical modifications that can be made to the base, phosphate and/or sugar moieties of the nucleic acid molecules described herein. Modifications that enhance their efficacy in cells, and removal of bases from nucleic acid molecules to shorten oligonucleotide synthesis times and reduce chemical requirements are desired.

There are several examples in the art describing sugar, base and phosphate modifications that can be introduced into nucleic acid molecules with significant enhancement in their nuclease stability and efficacy. For example, oligonucleotides are modified to enhance stability and/or enhance biological activity by modification with nuclease resistant groups, for example, 2′-amino, 2′-C-allyl, 2′-fluoro, 2′-O-methyl, 2′-O-allyl, 2′-H, nucleotide base modifications (for a review see Usman and Cedergren, 1992, TIBS. 17, 34; Usman et al., 1994, Nucleic Acids Symp. Ser. 31, 163; Burgin et al., 1996, Biochemistry, 35, 14090). Sugar modification of nucleic acid molecules have been extensively described in the art (see Eckstein et al., International Publication PCT No. WO 92/07065; Perrault et al. Nature, 1990, 344, 565-568; Pieken et al. Science, 1991, 253, 314-317; Usman and Cedergren, Trends in Biochem. Sci., 1992, 17, 334-339; Usman et al. International Publication PCT No. WO 93/15187; Sproat, U.S. Pat. No. 5,334,711 and Beigelman et al., 1995, J. Biol. Chem., 270, 25702; Beigelman et al., International PCT publication No. WO 97/26270; Beigelman et al., U.S. Pat. No. 5,716,824; Usman et al., U.S. Pat. No. 5,627,053; Woolf et al., International PCT Publication No. WO 98/13526; Thompson et al., U.S. Ser. No. 60/082,404 which was filed on Apr. 20, 1998; Karpeisky et al., 1998, Tetrahedron Lett., 39, 1131; Earnshaw and Gait, 1998, Biopolymers (Nucleic Acid Sciences), 48, 39-55; Verma and Eckstein, 1998, Annu. Rev. Biochem., 67, 99-134; and Burlina et al., 1997, Bioorg. Med. Chem., 5, 1999-2010; all of the references are hereby incorporated in their totality by reference herein). Such publications describe general methods and strategies to determine the location of incorporation of sugar, base and/or phosphate modifications and the like into nucleic acid molecules without modulating catalysis, and are incorporated by reference herein. In view of such teachings, similar modifications can be used as described herein to modify the siNA nucleic acid molecules of the instant invention so long as the ability of siNA to promote RNAi is cells is not significantly inhibited.

While chemical modification of oligonucleotide internucleotide linkages with phosphorothioate, phosphorodithioate, and/or 5′-methylphosphonate linkages improves stability, excessive modifications can cause some toxicity or decreased activity. Therefore, when designing nucleic acid molecules, the amount of these internucleotide linkages should be minimized. The reduction in the concentration of these linkages should lower toxicity, resulting in increased efficacy and higher specificity of these molecules.

Short interfering nucleic acid (siNA) molecules having chemical modifications that maintain or enhance activity are provided. Such a nucleic acid is also generally more resistant to nucleases than an unmodified nucleic acid. Accordingly, the in vitro and/or in vivo activity should not be significantly lowered. In cases in which modulation is the goal, therapeutic nucleic acid molecules delivered exogenously should optimally be stable within cells until translation of the target RNA has been modulated long enough to reduce the levels of the undesirable protein. This period of time varies between hours to days depending upon the disease state. Improvements in the chemical synthesis of RNA and DNA (Wincott et al., 1995, Nucleic Acids Res. 23, 2677; Caruthers et al., 1992, Methods in Enzymology 211, 3-19 (incorporated by reference herein)) have expanded the ability to modify nucleic acid molecules by introducing nucleotide modifications to enhance their nuclease stability, as described above.

In one embodiment, nucleic acid molecules of the invention include one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) G-clamp nucleotides. A G-clamp nucleotide is a modified cytosine analog wherein the modifications confer the ability to hydrogen bond both Watson-Crick and Hoogsteen faces of a complementary guanine within a duplex, see for example Lin and Matteucci, 1998, J. Am. Chem. Soc., 120, 8531-8532. A single G-clamp analog substitution within an oligonucleotide can result in substantially enhanced helical thermal stability and mismatch discrimination when hybridized to complementary oligonucleotides. The inclusion of such nucleotides in nucleic acid molecules of the invention results in both enhanced affinity and specificity to nucleic acid targets, complementary sequences, or template strands. In another embodiment, nucleic acid molecules of the invention include one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) LNA “locked nucleic acid” nucleotides such as a 2′,4′-C methylene bicyclo nucleotide (see for example Wengel et al., International PCT Publication No. WO 00/66604 and WO 99/14226).

In another embodiment, the invention features conjugates and/or complexes of siNA molecules of the invention. Such conjugates and/or complexes can be used to facilitate delivery of siNA molecules into a biological system, such as a cell. The conjugates and complexes provided by the instant invention can impart therapeutic activity by transferring therapeutic compounds across cellular membranes, altering the pharmacokinetics, and/or modulating the localization of nucleic acid molecules of the invention. The present invention encompasses the design and synthesis of novel conjugates and complexes for the delivery of molecules, including, but not limited to, small molecules, lipids, cholesterol, phospholipids, nucleosides, nucleotides, nucleic acids, antibodies, toxins, negatively charged polymers and other polymers, for example, proteins, peptides, hormones, carbohydrates, polyethylene glycols, or polyamines, across cellular membranes. In general, the transporters described are designed to be used either individually or as part of a multi-component system, with or without degradable linkers. These compounds are expected to improve delivery and/or localization of nucleic acid molecules of the invention into a number of cell types originating from different tissues, in the presence or absence of serum (see Sullenger and Cech, U.S. Pat. No. 5,854,038). Conjugates of the molecules described herein can be attached to biologically active molecules via linkers that are biodegradable, such as biodegradable nucleic acid linker molecules.

The term “biodegradable linker” as used herein, refers to a nucleic acid or non-nucleic acid linker molecule that is designed as a biodegradable linker to connect one molecule to another molecule, for example, a biologically active molecule to a siNA molecule of the invention or the sense and antisense strands of a siNA molecule of the invention. The biodegradable linker is designed such that its stability can be modulated for a particular purpose, such as delivery to a particular tissue or cell type. The stability of a nucleic acid-based biodegradable linker molecule can be modulated by using various chemistries, for example combinations of ribonucleotides, deoxyribonucleotides, and chemically-modified nucleotides, such as 2′-O-methyl, 2′-fluoro, 2′-amino, 2′-O-amino, 2′-C-allyl, 2′-O-allyl, and other 2′-modified or base modified nucleotides. The biodegradable nucleic acid linker molecule can be a dimer, trimer, tetramer or longer nucleic acid molecule, for example, an oligonucleotide of about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides in length, or can comprise a single nucleotide with a phosphorus-based linkage, for example, a phosphoramidate or phosphodiester linkage. The biodegradable nucleic acid linker molecule can also comprise nucleic acid backbone, nucleic acid sugar, or nucleic acid base modifications.

The term “biodegradable” as used herein, refers to degradation in a biological system, for example enzymatic degradation or chemical degradation.

The term “biologically active molecule” as used herein, refers to compounds or molecules that are capable of eliciting or modifying a biological response in a system. Non-limiting examples of biologically active siNA molecules either alone or in combination with other molecules contemplated by the instant invention include therapeutically active molecules such as antibodies, cholesterol, hormones, antivirals, peptides, proteins, chemotherapeutics, small molecules, vitamins, co-factors, nucleosides, nucleotides, oligonucleotides, enzymatic nucleic acids, antisense nucleic acids, triplex forming oligonucleotides, 2,5-A chimeras, siNA, dsRNA, allozymes, aptamers, decoys and analogs thereof. Biologically active molecules of the invention also include molecules capable of modulating the pharmacokinetics and/or pharmacodynamics of other biologically active molecules, for example, lipids and polymers such as polyamines, polyamides, polyethylene glycol and other polyethers.

The term “phospholipid” as used herein, refers to a hydrophobic molecule comprising at least one phosphorus group. For example, a phospholipid can comprise a phosphorus-containing group and saturated or unsaturated alkyl group, optionally substituted with OH, COOH, oxo, amine, or substituted or unsubstituted aryl groups.

Therapeutic nucleic acid molecules (e.g., siNA molecules) delivered exogenously optimally are stable within cells until reverse transcription of the RNA has been modulated long enough to reduce the levels of the RNA transcript. The nucleic acid molecules are resistant to nucleases in order to function as effective intracellular therapeutic agents. Improvements in the chemical synthesis of nucleic acid molecules described in the instant invention and in the art have expanded the ability to modify nucleic acid molecules by introducing nucleotide modifications to enhance their nuclease stability as described above.

In yet another embodiment, siNA molecules having chemical modifications that maintain or enhance enzymatic activity of proteins involved in RNAi are provided. Such nucleic acids are also generally more resistant to nucleases than unmodified nucleic acids. Thus, in vitro and/or in vivo the activity should not be significantly lowered.

Use of the nucleic acid-based molecules of the invention will lead to better treatment of the disease progression by affording the possibility of combination therapies (e.g., multiple siNA molecules targeted to different genes; nucleic acid molecules coupled with known small molecule modulators; or intermittent treatment with combinations of molecules, including different motifs and/or other chemical or biological molecules). The treatment of subjects with siNA molecules can also include combinations of different types of nucleic acid molecules, such as enzymatic nucleic acid molecules (ribozymes), allozymes, antisense, 2,5-A oligoadenylate, decoys, and aptamers.

In another aspect a siNA molecule of the invention comprises one or more 5′ and/or a 3′-cap structure, for example on only the sense siNA strand, the antisense siNA strand, or both siNA strands.

By “cap structure” is meant chemical modifications, which have been incorporated at either terminus of the oligonucleotide (see, for example, Adamic et al., U.S. Pat. No. 5,998,203, incorporated by reference herein). These terminal modifications protect the nucleic acid molecule from exonuclease degradation, and can help in delivery and/or localization within a cell. The cap can be present at the 5′-terminus (5′-cap) or at the 3′-terminal (3′-cap) or can be present on both termini. Non-limiting examples of the 5′-cap include, but are not limited to, glyceryl, inverted deoxy abasic residue (moiety); 4′,5′-methylene nucleotide; 1-(beta-D-erythrofuranosyl) nucleotide, 4′-thio nucleotide; carbocyclic nucleotide; 1,5-anhydrohexitol nucleotide; L-nucleotides; alpha-nucleotides; modified base nucleotide; phosphorodithioate linkage; threo-pentofuranosyl nucleotide; acyclic 3′,4′-seco nucleotide; acyclic 3,4-dihydroxybutyl nucleotide; acyclic 3,5-dihydroxypentyl nucleotide, 3′-3′-inverted nucleotide moiety; 3′-3′-inverted abasic moiety; 3′-2′-inverted nucleotide moiety; 3′-2′-inverted abasic moiety; 1,4-butanediol phosphate; 3′-phosphoramidate; hexylphosphate; aminohexyl phosphate; 3′-phosphate; 3′-phosphorothioate; phosphorodithioate; or bridging or non-bridging methylphosphonate moiety.

Non-limiting examples of the 3′-cap include, but are not limited to, glyceryl, inverted deoxy abasic residue (moiety), 4′,5′-methylene nucleotide; 1-(beta-D-erythrofuranosyl) nucleotide; 4′-thio nucleotide, carbocyclic nucleotide; 5′-amino-alkyl phosphate; 1,3-diamino-2-propyl phosphate; 3-aminopropyl phosphate; 6-aminohexyl phosphate; 1,2-aminododecyl phosphate; hydroxypropyl phosphate; 1,5-anhydrohexitol nucleotide; L-nucleotide; alpha-nucleotide; modified base nucleotide; phosphorodithioate; threo-pentofuranosyl nucleotide; acyclic 3′,4′-seco nucleotide; 3,4-dihydroxybutyl nucleotide; 3,5-dihydroxypentyl nucleotide, 5′-5′-inverted nucleotide moiety; 5′-5′-inverted abasic moiety; 5′-phosphoramidate; 5′-phosphorothioate; 1,4-butanediol phosphate; 5′-amino; bridging and/or non-bridging 5′-phosphoramidate, phosphorothioate and/or phosphorodithioate, bridging or non bridging methylphosphonate and 5′-mercapto moieties (for more details see Beaucage and Iyer, 1993, Tetrahedron 49, 1925; incorporated by reference herein).

By the term “non-nucleotide” is meant any group or compound which can be incorporated into a nucleic acid chain in the place of one or more nucleotide units, including either sugar and/or phosphate substitutions, and allows the remaining bases to exhibit their enzymatic activity. The group or compound is abasic in that it does not contain a commonly recognized nucleotide base, such as adenosine, guanine, cytosine, uracil or thymine and therefore lacks a base at the 1′-position.

An “alkyl” group refers to a saturated aliphatic hydrocarbon, including straight-chain, branched-chain, and cyclic alkyl groups. Preferably, the alkyl group has 1 to 12 carbons. More preferably, it is a lower alkyl of from 1 to 7 carbons, more preferably 1 to 4 carbons. The alkyl group can be substituted or unsubstituted. When substituted the substituted group(s) is preferably, hydroxyl, cyano, alkoxy, ═O, ═S, NO₂ or N(CH₃)₂, amino, or SH. The term also includes alkenyl groups that are unsaturated hydrocarbon groups containing at least one carbon-carbon double bond, including straight-chain, branched-chain, and cyclic groups. Preferably, the alkenyl group has 1 to 12 carbons. More preferably, it is a lower alkenyl of from 1 to 7 carbons, more preferably 1 to 4 carbons. The alkenyl group may be substituted or unsubstituted. When substituted the substituted group(s) is preferably, hydroxyl, cyano, alkoxy, ═O, ═S, NO₂, halogen, N(CH₃)₂, amino, or SH. The term “alkyl” also includes alkynyl groups that have an unsaturated hydrocarbon group containing at least one carbon-carbon triple bond, including straight-chain, branched-chain, and cyclic groups. Preferably, the alkynyl group has 1 to 12 carbons. More preferably, it is a lower alkynyl of from 1 to 7 carbons, more preferably 1 to 4 carbons. The alkynyl group may be substituted or unsubstituted. When substituted the substituted group(s) is preferably, hydroxyl, cyano, alkoxy, ═O, ═S, NO₂ or N(CH₃)₂, amino or SH.

Such alkyl groups can also include aryl, alkylaryl, carbocyclic aryl, heterocyclic aryl, amide and ester groups. An “aryl” group refers to an aromatic group that has at least one ring having a conjugated pi electron system and includes carbocyclic aryl, heterocyclic aryl and biaryl groups, all of which may be optionally substituted. The preferred substituent(s) of aryl groups are halogen, trihalomethyl, hydroxyl, SH, OH, cyano, alkoxy, alkyl, alkenyl, alkynyl, and amino groups. An “alkylaryl” group refers to an alkyl group (as described above) covalently joined to an aryl group (as described above). Carbocyclic aryl groups are groups wherein the ring atoms on the aromatic ring are all carbon atoms. The carbon atoms are optionally substituted. Heterocyclic aryl groups are groups having from 1 to 3 heteroatoms as ring atoms in the aromatic ring and the remainder of the ring atoms are carbon atoms. Suitable heteroatoms include oxygen, sulfur, and nitrogen, and include furanyl, thienyl, pyridyl, pyrrolyl, N-lower alkyl pyrrolo, pyrimidyl, pyrazinyl, imidazolyl and the like, all optionally substituted. An “amide” refers to an —C(O)—NH—R, where R is either alkyl, aryl, alkylaryl or hydrogen. An “ester” refers to an —C(O)—OR, where R is either alkyl, aryl, alkylaryl or hydrogen.

By “nucleotide” as used herein is as recognized in the art to include natural bases (standard), and modified bases well known in the art. Such bases are generally located at the 1′ position of a nucleotide sugar moiety. Nucleotides generally comprise a base, sugar and a phosphate group. The nucleotides can be unmodified or modified at the sugar, phosphate and/or base moiety, (also referred to interchangeably as nucleotide analogs, modified nucleotides, non-natural nucleotides, non-standard nucleotides and other; see, for example, Usman and McSwiggen, supra; Eckstein et al., International PCT Publication No. WO 92/07065; Usman et al., International PCT Publication No. WO 93/15187; Uhlman & Peyman, supra, all are hereby incorporated by reference herein). There are several examples of modified nucleic acid bases known in the art as summarized by Limbach et al., 1994, Nucleic Acids Res. 22, 2183. Some of the non-limiting examples of base modifications that can be introduced into nucleic acid molecules include, inosine, purine, pyridin-4-one, pyridin-2-one, phenyl, pseudouracil, 2,4,6-trimethoxy benzene, 3-methyl uracil, dihydrouridine, naphthyl, aminophenyl, 5-alkylcytidines (e.g., 5-methylcytidine), 5-alkyluridines (e.g., ribothymidine), 5-halouridine (e.g., 5-bromouridine) or 6-azapyrimidines or 6-alkylpyrimidines (e.g. 6-methyluridine), propyne, and others (Burgin et al., 1996, Biochemistry, 35, 14090; Uhlman & Peyman, supra). By “modified bases” in this aspect is meant nucleotide bases other than adenine, guanine, cytosine and uracil at 1′ position or their equivalents.

In one embodiment, the invention features modified siNA molecules, with phosphate backbone modifications comprising one or more phosphorothioate, phosphorodithioate, methylphosphonate, phosphotriester, morpholino, amidate carbamate, carboxymethyl, acetamidate, polyamide, sulfonate, sulfonamide, sulfamate, formacetal, thioformacetal, and/or alkylsilyl, substitutions. For a review of oligonucleotide backbone modifications, see Hunziker and Leumann, 1995, Nucleic Acid Analogues: Synthesis and Properties, in Modern Synthetic Methods, VCH, 331-417, and Mesmaeker et al., 1994, Novel Backbone Replacements for Oligonucleotides, in Carbohydrate Modifications in Antisense Research, ACS, 24-39.

By “abasic” is meant sugar moieties lacking a base or having other chemical groups in place of a base at the 1′ position, see for example Adamic et al., U.S. Pat. No. 5,998,203.

By “unmodified nucleoside” is meant one of the bases adenine, cytosine, guanine, thymine, or uracil joined to the 1′ carbon of β-D-ribo-furanose.

By “modified nucleoside” is meant any nucleotide base which contains a modification in the chemical structure of an unmodified nucleotide base, sugar and/or phosphate. Non-limiting examples of modified nucleotides are shown by Formulae I-VII and/or other modifications described herein.

In connection with 2′-modified nucleotides as described for the present invention, by “amino” is meant 2′-NH₂ or 2′-O—NH₂, which can be modified or unmodified. Such modified groups are described, for example, in Eckstein et al., U.S. Pat. No. 5,672,695 and Matulic-Adamic et al., U.S. Pat. No. 6,248,878, which are both incorporated by reference in their entireties.

Various modifications to nucleic acid siNA structure can be made to enhance the utility of these molecules. Such modifications will enhance shelf-life, half-life in vitro, stability, and ease of introduction of such oligonucleotides to the target site, e.g., to enhance penetration of cellular membranes, and confer the ability to recognize and bind to targeted cells.

Administration of Nucleic Acid Molecules

A siNA molecule of the invention can be adapted for use to treat, for example, oncology and proliferation related indications and conditions such as multidrug resistant cancers, breast cancer, cancers of the head and neck including various lymphomas such as mantle cell lymphoma, non-Hodgkins lymphoma, adenoma, squamous cell carcinoma, laryngeal carcinoma, cancers of the retina, cancers of the esophagus, multiple myeloma, ovarian cancer, melanoma, colorectal cancer, hepatocellular carcinoma, lung cancer, bladder cancer, pancreatic cancer, prostate cancer, glioblastoma; obesity and insulin resistance (e.g. type I and II diabetes); inflammatory disorders such as asthma, septic shock, rheumatoid arthritis, psoriasis, inflammatory bowl syndrome and any other diseases or conditions that are related to or will respond to the levels of MAP kinase in a cell or tissue, alone or in combination with other therapies. For example, a siNA molecule can comprise a delivery vehicle, including liposomes, for administration to a subject, carriers and diluents and their salts, and/or can be present in pharmaceutically acceptable formulations. Methods for the delivery of nucleic acid molecules are described in Akhtar et al., 1992, Trends Cell Bio., 2, 139; Delivery Strategies for Antisense Oligonucleotide Therapeutics, ed. Akhtar, 1995, Maurer et al., 1999, Mol. Membr. Biol., 16, 129-140; Hofland and Huang, 1999, Handb. Exp. Pharmacol., 137, 165-192; and Lee et al., 2000, ACS Symp. Ser., 752, 184-192, all of which are incorporated herein by reference. Beigelman et al., U.S. Pat. No. 6,395,713 and Sullivan et al., PCT WO 94/02595 further describe the general methods for delivery of nucleic acid molecules. These protocols can be utilized for the delivery of virtually any nucleic acid molecule. Nucleic acid molecules can be administered to cells by a variety of methods known to those of skill in the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as biodegradable polymers, hydrogels, cyclodextrins (see for example Gonzalez et al., 1999, Bioconjugate Chem., 10, 1068-1074), poly(lactic-co-glycolic)acid (PLGA) and PLCA microspheres (see for example U.S. Pat. No. 6,447,796 and US Patent Application Publication No. US 2002130430), biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors (O'Hare and Normand, International PCT Publication No. WO 00/53722). Alternatively, the nucleic acid/vehicle combination is locally delivered by direct injection or by use of an infusion pump. Direct injection of the nucleic acid molecules of the invention, whether subcutaneous, intramuscular, or intradermal, can take place using standard needle and syringe methodologies, or by needle-free technologies such as those described in Conry et al., 1999, Clin. Cancer Res., 5, 2330-2337 and Barry et al., International PCT Publication No. WO 99/31262. The molecules of the instant invention can be used as pharmaceutical agents. Pharmaceutical agents prevent, modulate the occurrence, or treat (alleviate a symptom to some extent, preferably all of the symptoms) of a disease state in a subject.

Thus, the invention features a pharmaceutical composition comprising one or more nucleic acid(s) of the invention in an acceptable carrier, such as a stabilizer, buffer, and the like. The polynucleotides of the invention can be administered (e.g., RNA, DNA or protein) and introduced into a subject by any standard means, with or without stabilizers, buffers, and the like, to form a pharmaceutical composition. When it is desired to use a liposome delivery mechanism, standard protocols for formation of liposomes can be followed. The compositions of the present invention can also be formulated and used as tablets, capsules or elixirs for oral administration, suppositories for rectal administration, sterile solutions, suspensions for injectable administration, and the other compositions known in the art.

The present invention also includes pharmaceutically acceptable formulations of the compounds described. These formulations include salts of the above compounds, e.g., acid addition salts, for example, salts of hydrochloric, hydrobromic, acetic acid, and benzene sulfonic acid.

A pharmacological composition or formulation refers to a composition or formulation in a form suitable for administration, e.g., systemic administration, into a cell or subject, including for example a human. Suitable forms, in part, depend upon the use or the route of entry, for example oral, transdermal, or by injection. Such forms should not prevent the composition or formulation from reaching a target cell (i.e., a cell to which the negatively charged nucleic acid is desirable for delivery). For example, pharmacological compositions injected into the blood stream should be soluble. Other factors are known in the art, and include considerations such as toxicity and forms that prevent the composition or formulation from exerting its effect.

By “systemic administration” is meant in vivo systemic absorption or accumulation of drugs in the blood stream followed by distribution throughout the entire body. Administration routes that lead to systemic absorption include, without limitation: intravenous, subcutaneous, intraperitoneal, inhalation, oral, intrapulmonary and intramuscular. Each of these administration routes exposes the siNA molecules of the invention to an accessible diseased tissue. The rate of entry of a drug into the circulation has been shown to be a function of molecular weight or size. The use of a liposome or other drug carrier comprising the compounds of the instant invention can potentially localize the drug, for example, in certain tissue types, such as the tissues of the reticular endothelial system (RES). A liposome formulation that can facilitate the association of drug with the surface of cells, such as, lymphocytes and macrophages is also useful. This approach can provide enhanced delivery of the drug to target cells by taking advantage of the specificity of macrophage and lymphocyte immune recognition of abnormal cells, such as cells producing excess MAP kinase.

By “pharmaceutically acceptable formulation” is meant a composition or formulation that allows for the effective distribution of the nucleic acid molecules of the instant invention in the physical location most suitable for their desired activity. Non-limiting examples of agents suitable for formulation with the nucleic acid molecules of the instant invention include: P-glycoprotein inhibitors (such as Pluronic P85), which can enhance entry of drugs into the CNS (Jolliet-Riant and Tillement, 1999, Fundam. Clin. Pharmacol., 13, 16-26); biodegradable polymers, such as poly (DL-lactide-coglycolide) microspheres for sustained release delivery after intracerebral implantation (Emerich, D F et al, 1999, Cell Transplant, 8, 47-58) (Alkermes, Inc. Cambridge, Mass.); and loaded nanoparticles, such as those made of polybutylcyanoacrylate, which can deliver drugs across the blood brain barrier and can alter neuronal uptake mechanisms (Prog Neuropsychopharmacol Biol Psychiatry, 23, 941-949, 1999). Other non-limiting examples of delivery strategies for the nucleic acid molecules of the instant invention include material described in Boado et al., 1998, J. Pharm. Sci., 87, 1308-1315; Tyler et al., 1999, FEBS Lett., 421, 280-284; Pardridge et al., 1995, PNAS USA., 92, 5592-5596; Boado, 1995, Adv. Drug Delivery Rev., 15, 73-107; Aldrian-Herrada et al., 1998, Nucleic Acids Res., 26, 4910-4916; and Tyler et al., 1999, PNAS USA., 96, 7053-7058.

The invention also features the use of the composition comprising surface-modified liposomes containing poly (ethylene glycol) lipids (PEG-modified, or long-circulating liposomes or stealth liposomes). These formulations offer a method for increasing the accumulation of drugs in target tissues. This class of drug carriers resists opsonization and elimination by the mononuclear phagocytic system (MPS or RES), thereby enabling longer blood circulation times and enhanced tissue exposure for the encapsulated drug (Lasic et al. Chem. Rev. 1995, 95, 2601-2627; Ishiwata et al., Chem. Pharm. Bull. 1995, 43, 1005-1011). Such liposomes have been shown to accumulate selectively in tumors, presumably by extravasation and capture in the neovascularized target tissues (Lasic et al., Science 1995, 267, 1275-1276; Oku et al., 1995, Biochim. Biophys. Acta, 1238, 86-90). The long-circulating liposomes enhance the pharmacokinetics and pharmacodynamics of DNA and RNA, particularly compared to conventional cationic liposomes which are known to accumulate in tissues of the MPS (Liu et al., J. Biol. Chem. 1995, 42, 24864-24870; Choi et al., International PCT Publication No. WO 96/10391; Ansell et al., International PCT Publication No. WO 96/10390; Holland et al., International PCT Publication No. WO 96/10392). Long-circulating liposomes are also likely to protect drugs from nuclease degradation to a greater extent compared to cationic liposomes, based on their ability to avoid accumulation in metabolically aggressive MPS tissues such as the liver and spleen.

The present invention also includes compositions prepared for storage or administration that include a pharmaceutically effective amount of the desired compounds in a pharmaceutically acceptable carrier or diluent. Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro edit. 1985), hereby incorporated by reference herein. For example, preservatives, stabilizers, dyes and flavoring agents can be provided. These include sodium benzoate, sorbic acid and esters of p-hydroxybenzoic acid. In addition, antioxidants and suspending agents can be used.

A pharmaceutically effective dose is that dose required to prevent, inhibit the occurrence, or treat (alleviate a symptom to some extent, preferably all of the symptoms) of a disease state. The pharmaceutically effective dose depends on the type of disease, the composition used, the route of administration, the type of mammal being treated, the physical characteristics of the specific mammal under consideration, concurrent medication, and other factors that those skilled in the medical arts will recognize. Generally, an amount between 0.1 mg/kg and 100 mg/kg body weight/day of active ingredients is administered dependent upon potency of the negatively charged polymer.

The nucleic acid molecules of the invention and formulations thereof can be administered orally, topically, parenterally, by inhalation or spray, or rectally in dosage unit formulations containing conventional non-toxic pharmaceutically acceptable carriers, adjuvants and/or vehicles. The term parenteral as used herein includes percutaneous, subcutaneous, intravascular (e.g., intravenous), intramuscular, or intrathecal injection or infusion techniques and the like. In addition, there is provided a pharmaceutical formulation comprising a nucleic acid molecule of the invention and a pharmaceutically acceptable carrier. One or more nucleic acid molecules of the invention can be present in association with one or more non-toxic pharmaceutically acceptable carriers and/or diluents and/or adjuvants, and if desired other active ingredients. The pharmaceutical compositions containing nucleic acid molecules of the invention can be in a form suitable for oral use, for example, as tablets, troches, lozenges, aqueous or oily suspensions, dispersible powders or granules, emulsion, hard or soft capsules, or syrups or elixirs.

Compositions intended for oral use can be prepared according to any method known to the art for the manufacture of pharmaceutical compositions and such compositions can contain one or more such sweetening agents, flavoring agents, coloring agents or preservative agents in order to provide pharmaceutically elegant and palatable preparations. Tablets contain the active ingredient in admixture with non-toxic pharmaceutically acceptable excipients that are suitable for the manufacture of tablets. These excipients can be, for example, inert diluents; such as calcium carbonate, sodium carbonate, lactose, calcium phosphate or sodium phosphate; granulating and disintegrating agents, for example, corn starch, or alginic acid; binding agents, for example starch, gelatin or acacia; and lubricating agents, for example magnesium stearate, stearic acid or talc. The tablets can be uncoated or they can be coated by known techniques. In some cases such coatings can be prepared by known techniques to delay disintegration and absorption in the gastrointestinal tract and thereby provide a sustained action over a longer period. For example, a time delay material such as glyceryl monostearate or glyceryl distearate can be employed.

Formulations for oral use can also be presented as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent, for example, calcium carbonate, calcium phosphate or kaolin, or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium, for example peanut oil, liquid paraffin or olive oil.

Aqueous suspensions contain the active materials in a mixture with excipients suitable for the manufacture of aqueous suspensions. Such excipients are suspending agents, for example sodium carboxymethylcellulose, methylcellulose, hydropropyl-methylcellulose, sodium alginate, polyvinylpyrrolidone, gum tragacanth and gum acacia; dispersing or wetting agents can be a naturally-occurring phosphatide, for example, lecithin, or condensation products of an alkylene oxide with fatty acids, for example polyoxyethylene stearate, or condensation products of ethylene oxide with long chain aliphatic alcohols, for example heptadecaethyleneoxycetanol, or condensation products of ethylene oxide with partial esters derived from fatty acids and a hexitol such as polyoxyethylene sorbitol monooleate, or condensation products of ethylene oxide with partial esters derived from fatty acids and hexitol anhydrides, for example polyethylene sorbitan monooleate. The aqueous suspensions can also contain one or more preservatives, for example ethyl, or n-propyl p-hydroxybenzoate, one or more coloring agents, one or more flavoring agents, and one or more sweetening agents, such as sucrose or saccharin.

Oily suspensions can be formulated by suspending the active ingredients in a vegetable oil, for example arachis oil, olive oil, sesame oil or coconut oil, or in a mineral oil such as liquid paraffin. The oily suspensions can contain a thickening agent, for example beeswax, hard paraffin or cetyl alcohol. Sweetening agents and flavoring agents can be added to provide palatable oral preparations. These compositions can be preserved by the addition of an anti-oxidant such as ascorbic acid

Dispersible powders and granules suitable for preparation of an aqueous suspension by the addition of water provide the active ingredient in admixture with a dispersing or wetting agent, suspending agent and one or more preservatives. Suitable dispersing or wetting agents or suspending agents are exemplified by those already mentioned above. Additional excipients, for example sweetening, flavoring and coloring agents, can also be present.

Pharmaceutical compositions of the invention can also be in the form of oil-in-water emulsions. The oily phase can be a vegetable oil or a mineral oil or mixtures of these. Suitable emulsifying agents can be naturally-occurring gums, for example gum acacia or gum tragacanth, naturally-occurring phosphatides, for example soy bean, lecithin, and esters or partial esters derived from fatty acids and hexitol, anhydrides, for example sorbitan monooleate, and condensation products of the said partial esters with ethylene oxide, for example polyoxyethylene sorbitan monooleate. The emulsions can also contain sweetening and flavoring agents.

Syrups and elixirs can be formulated with sweetening agents, for example glycerol, propylene glycol, sorbitol, glucose or sucrose. Such formulations can also contain a demulcent, a preservative and flavoring and coloring agents. The pharmaceutical compositions can be in the form of a sterile injectable aqueous or oleaginous suspension. This suspension can be formulated according to the known art using those suitable dispersing or wetting agents and suspending agents that have been mentioned above. The sterile injectable preparation can also be a sterile injectable solution or suspension in a non-toxic parentally acceptable diluent or solvent, for example as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that can be employed are water, Ringer's solution and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose, any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid find use in the preparation of injectables.

The nucleic acid molecules of the invention can also be administered in the form of suppositories, e.g., for rectal administration of the drug. These compositions can be prepared by mixing the drug with a suitable non-irritating excipient that is solid at ordinary temperatures but liquid at the rectal temperature and will therefore melt in the rectum to release the drug. Such materials include cocoa butter and polyethylene glycols.

Nucleic acid molecules of the invention can be administered parenterally in a sterile medium. The drug, depending on the vehicle and concentration used, can either be suspended or dissolved in the vehicle. Advantageously, adjuvants such as local anesthetics, preservatives and buffering agents can be dissolved in the vehicle.

Dosage levels of the order of from about 0.1 mg to about 140 mg per kilogram of body weight per day are useful in the treatment of the above-indicated conditions (about 0.5 mg to about 7 g per subject per day). The amount of active ingredient that can be combined with the carrier materials to produce a single dosage form varies depending upon the host treated and the particular mode of administration. Dosage unit forms generally contain between from about 1 mg to about 500 mg of an active ingredient.

It is understood that the specific dose level for any particular subject depends upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, sex, diet, time of administration, route of administration, and rate of excretion, drug combination and the severity of the particular disease undergoing therapy.

For administration to non-human animals, the composition can also be added to the animal feed or drinking water. It can be convenient to formulate the animal feed and drinking water compositions so that the animal takes in a therapeutically appropriate quantity of the composition along with its diet. It can also be convenient to present the composition as a premix for addition to the feed or drinking water.

The nucleic acid molecules of the present invention can also be administered to a subject in combination with other therapeutic compounds to increase the overall therapeutic effect. The use of multiple compounds to treat an indication can increase the beneficial effects while reducing the presence of side effects.

In one embodiment, the invention comprises compositions suitable for administering nucleic acid molecules of the invention to specific cell types. For example, the asialoglycoprotein receptor (ASGPr) (Wu and Wu, 1987, J. Biol. Chem. 262, 4429-4432) is unique to hepatocytes and binds branched galactose-terminal glycoproteins, such as asialoorosomucoid (ASOR). In another example, the folate receptor is overexpressed in many cancer cells. Binding of such glycoproteins, synthetic glycoconjugates, or folates to the receptor takes place with an affinity that strongly depends on the degree of branching of the oligosaccharide chain, for example, triatennary structures are bound with greater affinity than biatenarry or monoatennary chains (Baenziger and Fiete, 1980, Cell, 22, 611-620; Connolly et al., 1982, J. Biol. Chem., 257, 939-945). Lee and Lee, 1987, Glycoconjugate J., 4, 317-328, obtained this high specificity through the use of N-acetyl-D-galactosamine as the carbohydrate moiety, which has higher affinity for the receptor, compared to galactose. This “clustering effect” has also been described for the binding and uptake of mannosyl-terminating glycoproteins or glycoconjugates (Ponpipom et al., 1981, J. Med. Chem., 24, 1388-1395). The use of galactose, galactosamine, or folate based conjugates to transport exogenous compounds across cell membranes can provide a targeted delivery approach to, for example, the treatment of liver disease, cancers of the liver, or other cancers. The use of bioconjugates can also provide a reduction in the required dose of therapeutic compounds required for treatment. Furthermore, therapeutic bioavailability, pharmacodynamics, and pharmacokinetic parameters can be modulated through the use of nucleic acid bioconjugates of the invention. Non-limiting examples of such bioconjugates are described in Vargeese et al., U.S. Ser. No. 10/201,394, filed Aug. 13, 2001; and Matulic-Adamic et al., U.S. Ser. No. 60/362,016, filed Mar. 6, 2002.

Alternatively, certain siNA molecules of the instant invention can be expressed within cells from eukaryotic promoters (e.g., Izant and Weintraub, 1985, Science, 229, 345; McGarry and Lindquist, 1986, Proc. Natl. Acad. Sci., USA 83, 399; Scanlon et al., 1991, Proc. Natl. Acad. Sci. USA, 88, 10591-5; Kashani-Sabet et al., 1992, Antisense Res. Dev., 2, 3-15; Dropulic et al., 1992, J. Virol., 66, 1432-41; Weerasinghe et al., 1991, J. Virol., 65, 5531-4; Ojwang et al., 1992, Proc. Natl. Acad. Sci. USA, 89, 10802-6; Chen et al., 1992, Nucleic Acids Res., 20, 4581-9; Sarver et al., 1990 Science, 247, 1222-1225; Thompson et al., 1995, Nucleic Acids Res., 23, 2259; Good et al., 1997, Gene Therapy, 4, 45. Those skilled in the art realize that any nucleic acid can be expressed in eukaryotic cells from the appropriate DNA/RNA vector. The activity of such nucleic acids can be augmented by their release from the primary transcript by an enzymatic nucleic acid (Draper et al., PCT WO 93/23569, and Sullivan et al., PCT WO 94/02595; Ohkawa et al., 1992, Nucleic Acids Symp. Ser., 27, 15-6; Taira et al., 1991, Nucleic Acids Res., 19, 5125-30; Ventura et al., 1993, Nucleic Acids Res., 21, 3249-55; Chowrira et al., 1994, J. Biol. Chem., 269, 25856.

In another aspect of the invention, RNA molecules of the present invention can be expressed from transcription units (see for example Couture et al., 1996, TIG., 12, 510) inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. siNA expressing viral vectors can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. In another embodiment, pol III based constructs are used to express nucleic acid molecules of the invention (see for example Thompson, U.S. Pats. Nos. 5,902,880 and 6,146,886). The recombinant vectors capable of expressing the siNA molecules can be delivered as described above, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of nucleic acid molecules. Such vectors can be repeatedly administered as necessary. Once expressed, the siNA molecule interacts with the target mRNA and generates an RNAi response. Delivery of siNA molecule expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell (for a review see Couture et al., 1996, TIG., 12, 510).

In one aspect the invention features an expression vector comprising a nucleic acid sequence encoding at least one siNA molecule of the instant invention. The expression vector can encode one or both strands of a siNA duplex, or a single self-complementary strand that self hybridizes into a siNA duplex. The nucleic acid sequences encoding the siNA molecules of the instant invention can be operably linked in a manner that allows expression of the siNA molecule (see for example Paul et al., 2002, Nature Biotechnology, 19, 505; Miyagishi and Taira, 2002, Nature Biotechnology, 19, 497; Lee et al., 2002, Nature Biotechnology, 19, 500; and Novina et al., 2002, Nature Medicine, advance online publication doi:10.1038/nm725).

In another aspect, the invention features an expression vector comprising: a) a transcription initiation region (e.g., eukaryotic pol I, II or III initiation region); b) a transcription termination region (e.g., eukaryotic pol I, II or III termination region); and c) a nucleic acid sequence encoding at least one of the siNA molecules of the instant invention, wherein said sequence is operably linked to said initiation region and said termination region in a manner that allows expression and/or delivery of the siNA molecule. The vector can optionally include an open reading frame (ORF) for a protein operably linked on the 5′ side or the 3′-side of the sequence encoding the siNA of the invention and/or an intron (intervening sequences).

Transcription of the siNA molecule sequences can be driven from a promoter for eukaryotic RNA polymerase I (pol I), RNA polymerase II (pol II), or RNA polymerase III (pol III). Transcripts from pol II or pol III promoters are expressed at high levels in all cells; the levels of a given pol II promoter in a given cell type depends on the nature of the gene regulatory sequences (enhancers, silencers, etc.) present nearby. Prokaryotic RNA polymerase promoters are also used, providing that the prokaryotic RNA polymerase enzyme is expressed in the appropriate cells (Elroy-Stein and Moss, 1990, Proc. Natl. Acad. Sci. USA, 87, 6743-7; Gao and Huang 1993, Nucleic Acids Res., 21, 2867-72; Lieber et al., 1993, Methods Enzymol., 217, 47-66; Zhou et al., 1990, Mol. Cell. Biol., 10, 4529-37). Several investigators have demonstrated that nucleic acid molecules expressed from such promoters can function in mammalian cells (e.g. Kashani-Sabet et al., 1992, Antisense Res. Dev., 2, 3-15; Ojwang et al., 1992, Proc. Natl. Acad. Sci. USA, 89, 10802-6; Chen et al., 1992, Nucleic Acids Res., 20, 4581-9; Yu et al., 1993, Proc. Natl. Acad. Sci. USA, 90, 6340-4; L'Huillier et al., 1992, EMBO J., 11, 4411-8; Lisziewicz et al., 1993, Proc. Natl. Acad. Sci. U.S. A, 90, 8000-4; Thompson et al., 1995, Nucleic Acids Res., 23, 2259; Sullenger & Cech, 1993, Science, 262, 1566). More specifically, transcription units such as the ones derived from genes encoding U6 small nuclear (snRNA), transfer RNA (tRNA) and adenovirus VA RNA are useful in generating high concentrations of desired RNA molecules such as siNA in cells (Thompson et al., supra; Couture and Stinchcomb, 1996, supra; Noonberg et al., 1994, Nucleic Acid Res., 22, 2830; Noonberg et al., U.S. Pat. No. 5,624,803; Good et al., 1997, Gene Ther., 4, 45; Beigelman et al., International PCT Publication No. WO 96/18736. The above siNA transcription units can be incorporated into a variety of vectors for introduction into mammalian cells, including but not restricted to, plasmid DNA vectors, viral DNA vectors (such as adenovirus or adeno-associated virus vectors), or viral RNA vectors (such as retroviral or alphavirus vectors) (for a review see Couture and Stinchcomb, 1996, supra).

In another aspect the invention features an expression vector comprising a nucleic acid sequence encoding at least one of the siNA molecules of the invention in a manner that allows expression of that siNA molecule. The expression vector comprises in one embodiment; a) a transcription initiation region; b) a transcription termination region; and c) a nucleic acid sequence encoding at least one strand of the siNA molecule, wherein the sequence is operably linked to the initiation region and the termination region in a manner that allows expression and/or delivery of the siNA molecule.

In another embodiment the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an open reading frame; and d) a nucleic acid sequence encoding at least one strand of a siNA molecule, wherein the sequence is operably linked to the 3′-end of the open reading frame and wherein the sequence is operably linked to the initiation region, the open reading frame and the termination region in a manner that allows expression and/or delivery of the siNA molecule. In yet another embodiment, the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; and d) a nucleic acid sequence encoding at least one siNA molecule, wherein the sequence is operably linked to the initiation region, the intron and the termination region in a manner which allows expression and/or delivery of the nucleic acid molecule.

In another embodiment, the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; d) an open reading frame; and e) a nucleic acid sequence encoding at least one strand of a siNA molecule, wherein the sequence is operably linked to the 3′-end of the open reading frame and wherein the sequence is operably linked to the initiation region, the intron, the open reading frame and the termination region in a manner which allows expression and/or delivery of the siNA molecule.

MAP Kinase Biology and Biochemistry

The mitogen-activated protein kinases (MAPKs) have been at the forefront of a rapid advance in the understanding of cellular events in growth factor and cytokine receptor signaling. The MAP kinases (also referred to as extracellular signal-regulated protein kinases, or ERKs) are the terminal enzymes in a three-kinase cascade. The reiteration of three-kinase cascades for related but distinct signaling pathways gave rise to the concept of a MAPK pathway as a modular, multifunctional signaling element that acts sequentially within one pathway, where each enzyme phosphorylates and thereby activates the next member in the sequence. A typical MAPK pathway thus consists of three protein kinases: a MAPK kinase kinase (or MEKK) that activates a MAPK kinase (or MEK) which, in turn, activates a MAPK/ERK enzyme. Each of the MAPK/ERK, JNK and p38 cascades consists of a three-enzyme module that includes MEKK, MEK and an ERK or MAPK superfamily member. A variety of extracellular signals triggers initial events upon association with their respective cell surface receptors and this signal is then transmitted to the interior of the cell where it activates the appropriate cascades (see for example FIG. 12).

The identification of distinct MAPK cascades that are conserved across all eukaryotes indicates that the MAPK module has been adapted for interpretation of a diverse array of extracellular signals. Although mitogen activation of the MAPK subfamily (e.g., ERK1 and ERK2) has dominated efforts to understand MAPK signaling, increasing appreciation of the role of the stress-activated kinases, JNK and p38, illustrates the diverse nature of the MAPK superfamily of enzymes. Although sequence similarities among components of the individual MAPK modules used for activation of ERK1/2, JNKs and p38 are considerable, the fidelity that is maintained in order to translate specific extracellular signals into discrete physiological responses illustrates the selective adaptation of each MAPK pathway. The MAPK superfamily of enzymes is a critical component cellular regulative processes that coordinates incoming signals generated by a variety of extracellular and intracellular mediators. Specific phosphorylation and activation of enzymes in the MAPK pathway transmits the signal down the cascade, resulting in phosphorylation of many proteins with substantial regulatory functions throughout the cell, including other protein kinases, transcription factors, cytoskeletal proteins and other enzymes. The diversity of signals that culminates in MAPK activation indicates that these enzymes are not dedicated to regulation of any single growth factor, hormone or cytokine system. Instead, MAPKs—like cAMP-dependent protein kinase (PKA) and Ca²⁺- and phospholipid-dependent protein kinases (PKC) serve many signaling purposes. Because activation of the MAPK pathways are triggered to varying extents by a large number of receptor systems, temporal and spatial differences are critical to determining ligand- and cell-type-specific functions.

Following activation of cells with an appropriate extracellular stimuli, the signal is transmitted to the canonical MAPK module comprising three protein kinases. The progression of events for each enzyme cascade is the same, although specific isoforms of each enzyme appear to confer the required specificity within each pathway. The first enzyme in the module is a MEKK enzyme, of which Raf and its isoforms are one example. The MEKK enzymes comprise Ser/Thr protein kinases that activate the MEK enzymes by phosphorylating two serine or threonine residues within a Ser-X-X-X-Ser/Thr motif. Once activated, the MEK enzymes, which are hybrid function Ser/Thr/Tyr protein kinases, phosphorylate the MAPK/ERK enzymes on Thr and Tyr residues within the Thr-X-Tyr (TXY) consensus sequence. A critical and common feature of the MAPK superfamily of enzymes is that they are activated upon dual phosphorylation within a TXY consensus sequence present in the activation loop of the catalytic domain. The central amino acid differs for each MAPK superfamily member, corresponding to Glu for ERK1/2, Gly for p38/HOG and Pro for JNK/SAPK, although MEK specificity is not limited to these particular residues. Phosphorylation at only one of the two positions does not appear to activate the enzyme, although it may prime the kinase domain for receipt of the second phosphorylation event.

ERK1 and ERK2 were the first members of the MAPK superfamily whose cDNAs were cloned and the signaling cascades that lead to their activation characterized. Potent activation of ERK1 and ERK2 can be initiated through activation of transmembrane receptors with intrinsic protein tyrosine kinase (PTK) activity. Binding of extracellular ligands to their respective cell surface receptors results in receptor autophosphorylation and enhanced PTK activity. The subsequent association of the Src homology 2 (SH2) domains of adaptor proteins such as Grb2 and Shc with the autophosphorylated receptors, or with additional docking proteins, provides the molecular interactions that bring the required signal transduction molecules into close proximity with each other. Receptors without intrinsic PTK activity but which comprise sites for tyrosine phosphorylation can also activate the cascade via association of their phosphotyrosine residues with adaptor molecules. For example, the SH3 domain of Grb2 binds a proline-rich region of the guanine nucleotide-exchange protein SOS which, in turn, increases the association of Ras with GTP. The GTP-bound form of Ras binds to Raf (a MAPK kinase) isoforms, including C-Raf-1, B-Raf and A-Raf. This action targets Raf to the membrane, where its protein kinase activity is increased by phosphorylation. MAPK kinases (MEK1 and MEK2), are phosphorylated and activated by Raf. MEK1 and MEK2 are dual-specificity protein kinases that dually phosphorylate the ERK enzymes (corresponding to Thr¹⁸³ and Tyr¹⁸⁵ of p42ERK2), thereby increasing their enzymatic activity by approximately 1,000-fold over the activity found with the basal or monophosphorylated forms. Phosphorylation of these residues causes closure of the kinase active site and induces conformational changes necessary for high activity.

MAPK mutants, lacking either a lysine required for catalytic activity or the prerequisite TXY phosphorylation sites, can inhibit signaling by the native enzymes in cells. In the case of ERK1 and ERK2, these mutants have been used with repeated success. For example, mutant ERK2 completely blocks proliferation in response to epidermal growth factor (EGF) and v-Raf, and partially blocks induction by serum or small t antigen. ERK1 antisense mRNA and an ERK1 phosphorylation site mutants interfere with thrombin-induced transcription as well as serum-dependent proliferation. These findings suggest an essential role in proliferation and transformation for the ERK/MAPK pathway.

The JNK/SAPK and p38/HOG pathways are activated by ultraviolet light, cytokines, osmotic shock, inhibitors of DNA, RNA, and protein synthesis, and to a lesser extent by certain growth factors. This spectrum of regulators suggests that the enzymes are transducers of a variety of cellular stress responses. In contrast to activation of ERK1 and ERK2, upstream signal transduction mechanisms for the JNK and p38 cascades are less well understood. When transfected into mammalian cells, a diverse group of protein kinases including the mixed lineage kinases (MLKs) and relatives of the yeast Step 20p, such as the p21-activated kinases (PAKs) and germinal center kinase (GCK), cause activation of JNK/SAPK. Similarly, GTP-bound forms of the small GTP-binding proteins, Rac and Cdc42, activate the JNK/SAPK pathway and, to a lesser extent, the p38 pathway. Direct activation of both pathways by PAKs also has been demonstrated, suggesting that PAKs can be the relevant effectors for these small G proteins. The PAKs are homologs of the yeast kinases Step 20p and Shk1, enzymes upstream of the MAPK modules in yeast pheromone response pathways. Both yeast and mammalian protein kinases contain a binding site for Rac/Cdc42 and share the property of being activated in vitro through association with these small G proteins when in their GTP-bound states. In yeast, Step 20p is thought to phosphorylate and activate the MEKK isoform Ste11p, suggesting that MEKKs may be PAK targets. This summary of MAP kinase pathways has been adapted from Cobb and Schaefer, 1996, Promega Notes Magazine Number 59, page 37.

The regulation of c-Jun transcriptional activity by Jun N-terminal kinase (JNK), ERK1, ERK2, and p38 kinases has become a paradigm for the understanding of how mitogen-activated protein (MAP) kinase signaling pathways elicit specific changes in gene transcription through selective phosphorylation of nuclear transcription factors. Selective phosphorylation of c-Jun by JNK is detected by a specific docking motif in c-Jun, the delta region, which enables JNK to physically interact with c-Jun. Analogous MAP kinase docking motifs have subsequently been found in several other transcription factors, indicating that this is a general mechanism for ensuring the specificity of signal transduction. Furthermore, genetic and biochemical studies in mice, flies and cultured cells have provided evidence that signals relayed by JNK through c-Jun regulate a wide range of cellular processes including cell proliferation, tumorigenesis, apoptosis and embryonic development. Despite these advances, in most cases, the genes or programs of gene expression downstream of JNK and c-Jun, which control these processes, have yet to be defined. One important process that is associated with JNK gene expression is the development of insulin resistance in obese subjects.

Obesity is closely associated with insulin resistance and establishes the leading risk factor for type 2 diabetes mellitus in mammals. The c-Jun amino-terminal kinases (JNKs) can interfere with insulin activity in cultured cells and are activated by inflammatory cytokines and free fatty acids molecules that have been implicated in the development of type 2 diabetes. Hirosumi et al, 2002, Nature, 420, 333-336, demonstrate that JNK activity is abnormally elevated in obesity. Furthermore, Hirosumi et al, supra have shown that an absence of JNK1 results in decreased adiposity with significantly improved insulin sensitivity and enhanced insulin receptor capacity in two different models of mouse obesity. Thus, JNK is a crucial mediator of obesity and insulin resistance and as such, provides a potential target for nucleic acid based therapeutics that modulate JNK gene expression.

The transcription factor and oncogene, c-JUN, is implicated in several critical cell processes including cell proliferation, cell survival, and oncogenic transformation. Although it is broadly expressed in a wide variety of cell types, it plays an especially important role in hepatocytes. However, the precise role played by c-JUN in hepatocytes seems to depend on the differentiation state of this cell type. Adult differentiated hepatocytes depend on c-JUN for progression through the cell cycle. Deletion of c-JUN reduces the proliferation capacity of hepatocytes following partial hepatectomy. c-JUN is thought to be major component in the development of human hepatocellular carcinoma (HCC). HCC is the most common form of primary liver cancer. Chronic HCV infection is a major risk factor for HCC.

The role of c-JUN in liver cancer has recently been investigated (Eferl et al., 2003, Cell, 112, 181). These investigators deleted c-JUN and then induced liver cancer by chemical carcinogenesis. They observed that deletion of c-JUN dramatically interfered with liver tumor formation. Animal survival was markedly worse in c-JUN wild-type animals relative to deletion mutants. In particular, the number of apoptotic cells increased about five fold in tumors in the c-JUN deletion strain relative to the wild-type animals. Importantly, levels of the pro-apoptotic gene products such as p53 and noxa were elevated in the c-JUN deletion strain. c-JUN is likely to antagonize other pro-apoptotic genes such as TNF-a. Thus, by blocking p53 and its large family of dependent genes, c-JUN seems to promote tumor formation. Since a large fraction of chronically infected HCV patients develop hepatocellular carcinoma, c-JUN provides an attractive target for treating HCV infected patients to prevent or ameliorate hepatocellular carcinoma.

Based upon the current understanding of MAP kinase pathways, the modulation of MAP kinase pathways is instrumental in the development of new therapeutics in, for example, the fields of inflammation, oncology, and metabolism. As such, modulation of a specific MAP kinase pathway using small interfering nucleic acid (siNA) mediated RNAi represents a novel approach to the treatment and study of diseases and conditions related to a specific MAP kinase activity and/or gene expression.

EXAMPLES

The following are non-limiting examples showing the selection, isolation, synthesis and activity of nucleic acids of the instant invention.

Example 1 Tandem Synthesis of siNA Constructs

Exemplary siNA molecules of the invention are synthesized in tandem using a cleavable linker, for example, a succinyl-based linker. Tandem synthesis as described herein is followed by a one-step purification process that provides RNAi molecules in high yield. This approach is highly amenable to siNA synthesis in support of high throughput RNAi screening, and can be readily adapted to multi-column or multi-well synthesis platforms.

After completing a tandem synthesis of a siNA oligo and its complement in which the 5′-terminal dimethoxytrityl (5′-O-DMT) group remains intact (trityl on synthesis), the oligonucleotides are deprotected as described above. Following deprotection, the siNA sequence strands are allowed to spontaneously hybridize. This hybridization yields a duplex in which one strand has retained the 5′-O-DMT group while the complementary strand comprises a terminal 5′-hydroxyl. The newly formed duplex behaves as a single molecule during routine solid-phase extraction purification (Trityl-On purification) even though only one molecule has a dimethoxytrityl group. Because the strands form a stable duplex, this dimethoxytrityl group (or an equivalent group, such as other trityl groups or other hydrophobic moieties) is all that is required to purify the pair of oligos, for example, by using a C18 cartridge.

Standard phosphoramidite synthesis chemistry is used up to the point of introducing a tandem linker, such as an inverted deoxy abasic succinate or glyceryl succinate linker (see FIG. 1) or an equivalent cleavable linker. A non-limiting example of linker coupling conditions that can be used includes a hindered base such as diisopropylethylamine (DIPA) and/or DMAP in the presence of an activator reagent such as Bromotripyrrolidinophosphoniumhexafluororophosphate (PyBrOP). After the linker is coupled, standard synthesis chemistry is utilized to complete synthesis of the second sequence leaving the terminal the 5′-O-DMT intact. Following synthesis, the resulting oligonucleotide is deprotected according to the procedures described herein and quenched with a suitable buffer, for example with 50 mM NaOAc or 1.5M NH₄H₂CO₃.

Purification of the siNA duplex can be readily accomplished using solid phase extraction, for example using a Waters C18 SepPak Ig cartridge conditioned with 1 column volume (CV) of acetonitrile, 2 CV H₂O, and 2 CV 50 mM NaOAc. The sample is loaded and then washed with 1 CV H₂O or 50 mM NaOAc. Failure sequences are eluted with 1 CV 14% ACN (Aqueous with 50 mM NaOAc and 50 mM NaCl). The column is then washed, for example with 1 CV H₂O followed by on-column detritylation, for example by passing 1 CV of 1% aqueous trifluoroacetic acid (TFA) over the column, then adding a second CV of 1% aqueous TFA to the column and allowing to stand for approximately 10 minutes. The remaining TFA solution is removed and the column washed with H₂O followed by 1 CV 1M NaCl and additional H₂O. The siNA duplex product is then eluted, for example, using 1 CV 20% aqueous CAN.

FIG. 2 provides an example of MALDI-TOF mass spectrometry analysis of a purified siNA construct in which each peak corresponds to the calculated mass of an individual siNA strand of the siNA duplex. The same purified siNA provides three peaks when analyzed by capillary gel electrophoresis (CGE), one peak presumably corresponding to the duplex siNA, and two peaks presumably corresponding to the separate siNA sequence strands. Ion exchange HPLC analysis of the same siNA contract only shows a single peak. Testing of the purified siNA construct using a luciferase reporter assay described below demonstrated the same RNAi activity compared to siNA constructs generated from separately synthesized oligonucleotide sequence strands.

Example 2 Identification of Potential siNA Target Sites in Any RNA Sequence

The sequence of an RNA target of interest, such as a viral or human mRNA transcript, is screened for target sites, for example by using a computer folding algorithm. In a non-limiting example, the sequence of a gene or RNA gene transcript derived from a database, such as Genbank, is used to generate siNA targets having complementarity to the target. Such sequences can be obtained from a database, or can be determined experimentally as known in the art. Target sites that are known, for example, those target sites determined to be effective target sites based on studies with other nucleic acid molecules, for example ribozymes or antisense, or those targets known to be associated with a disease or condition such as those sites containing mutations or deletions, can be used to design siNA molecules targeting those sites. Various parameters can be used to determine which sites are the most suitable target sites within the target RNA sequence. These parameters include but are not limited to secondary or tertiary RNA structure, the nucleotide base composition of the target sequence, the degree of homology between various regions of the target sequence, or the relative position of the target sequence within the RNA transcript. Based on these determinations, any number of target sites within the RNA transcript can be chosen to screen siNA molecules for efficacy, for example by using in vitro RNA cleavage assays, cell culture, or animal models. In a non-limiting example, anywhere from 1 to 1000 target sites are chosen within the transcript based on the size of the siNA construct to be used. High throughput screening assays can be developed for screening siNA molecules using methods known in the art, such as with multi-well or multi-plate assays to determine efficient reduction in target gene expression.

Example 3 Selection of siNA Molecule Target Sites in a RNA

The following non-limiting steps can be used to carry out the selection of siNAs targeting a given gene sequence or transcript.

1. The target sequence is parsed in silico into a list of all fragments or subsequences of a particular length, for example 23 nucleotide fragments, contained within the target sequence. This step is typically carried out using a custom Perl script, but commercial sequence analysis programs such as Oligo, MacVector, or the GCG Wisconsin Package can be employed as well.

2. In some instances the siNAs correspond to more than one target sequence; such would be the case for example in targeting different transcripts of the same gene, targeting different transcripts of more than one gene, or for targeting both the human gene and an animal homolog. In this case, a subsequence list of a particular length is generated for each of the targets, and then the lists are compared to find matching sequences in each list. The subsequences are then ranked according to the number of target sequences that contain the given subsequence; the goal is to find subsequences that are present in most or all of the target sequences. Alternately, the ranking can identify subsequences that are unique to a target sequence, such as a mutant target sequence. Such an approach would enable the use of siNA to target specifically the mutant sequence and not effect the expression of the normal sequence.

3. In some instances the siNA subsequences are absent in one or more sequences while present in the desired target sequence; such would be the case if the siNA targets a gene with a paralogous family member that is to remain untargeted. As in case 2 above, a subsequence list of a particular length is generated for each of the targets, and then the lists are compared to find sequences that are present in the target gene but are absent in the untargeted paralog.

4. The ranked siNA subsequences can be further analyzed and ranked according to GC content. A preference can be given to sites containing 30-70% GC, with a further preference to sites containing 40-60% GC.

5. The ranked siNA subsequences can be further analyzed and ranked according to self-folding and internal hairpins. Weaker internal folds are preferred; strong hairpin structures are to be avoided.

6. The ranked siNA subsequences can be further analyzed and ranked according to whether they have runs of GGG or CCC in the sequence. GGG (or even more Gs) in either strand can make oligonucleotide synthesis problematic and can potentially interfere with RNAi activity, so it is avoided whenever better sequences are available. CCC is searched in the target strand because that will place GGG in the antisense strand.

7. The ranked siNA subsequences can be further analyzed and ranked according to whether they have the dinucleotide UU (uridine dinucleotide) on the 3′-end of the sequence, and/or AA on the 5′-end of the sequence (to yield 3′ UU on the antisense sequence). These sequences allow one to design siNA molecules with terminal TT thymidine dinucleotides.

8. Four or five target sites are chosen from the ranked list of subsequences as described above. For example, in subsequences having 23 nucleotides, the right 21 nucleotides of each chosen 23-mer subsequence are then designed and synthesized for the upper (sense) strand of the siNA duplex, while the reverse complement of the left 21 nucleotides of each chosen 23-mer subsequence are then designed and synthesized for the lower (antisense) strand of the siNA duplex (see Tables II and III). If terminal TT residues are desired for the sequence (as described in paragraph 7), then the two 3′ terminal nucleotides of both the sense and antisense strands are replaced by TT prior to synthesizing the oligos.

9. The siNA molecules are screened in an in vitro, cell culture or animal model system to identify the most active siNA molecule or the most preferred target site within the target RNA sequence.

In an alternate approach, a pool of siNA constructs specific to a MAP kinase target sequence is used to screen for target sites in cells expressing MAP kinase (e.g., c-JUN) RNA, such as human kidney fibroblast (e.g., 293 cells), HeLa, or HepG2 cells. The general strategy used in this approach is shown in FIG. 9. A non-limiting example of such as pool is a pool comprising sequences having sense sequences comprising SEQ ID NOs. 1247-1427 and antisense sequences comprising SEQ ID NOs. 1428-1608 respectively. 293, HeLa, or HepG2 cells expressing MAP kinase (e.g., c-JUN) are transfected with the pool of siNA constructs and cells that demonstrate a phenotype associated with MAP kinase (e.g., c-JUN) inhibition are sorted. The pool of siNA constructs can be expressed from transcription cassettes inserted into appropriate vectors (see for example FIG. 7 and FIG. 8). The siNA from cells demonstrating a positive phenotypic change (e.g., decreased proliferation, decreased MAP kinase (e.g., c-JUN) mRNA levels or decreased MAP kinase (e.g., c-JUN) protein expression), are sequenced to determine the most suitable target site(s) within the target MAP kinase (e.g., c-JUN) RNA sequence.

Example 4 MAP Kinase Targeted siNA Design

siNA target sites were chosen by analyzing sequences of the MAP kinase (e.g., c-JUN) RNA target and optionally prioritizing the target sites on the basis of folding (structure of any given sequence analyzed to determine siNA accessibility to the target), by using a library of siNA molecules as described in Example 3, or alternately by using an in vitro siNA system as described in Example 6 herein. siNA molecules were designed that could bind each target and are optionally individually analyzed by computer folding to assess whether the siNA molecule can interact with the target sequence. Varying the length of the siNA molecules can be chosen to optimize activity. Generally, a sufficient number of complementary nucleotide bases are chosen to bind to, or otherwise interact with, the target RNA, but the degree of complementarity can be modulated to accommodate siNA duplexes or varying length or base composition. By using such methodologies, siNA molecules can be designed to target sites within any known RNA sequence, for example those RNA sequences corresponding to the any gene transcript.

Chemically modified siNA constructs are designed to provide nuclease stability for systemic administration in vivo and/or improved pharmacokinetic, localization, and delivery properties while preserving the ability to mediate RNAi activity. Chemical modifications as described herein are introduced synthetically using synthetic methods described herein and those generally known in the art. The synthetic siNA constructs are then assayed for nuclease stability in serum and/or cellular/tissue extracts (e.g. liver extracts). The synthetic siNA constructs are also tested in parallel for RNAi activity using an appropriate assay, such as a luciferase reporter assay as described herein or another suitable assay that can quantity RNAi activity. Synthetic siNA constructs that possess both nuclease stability and RNAi activity can be further modified and re-evaluated in stability and activity assays. The chemical modifications of the stabilized active siNA constructs can then be applied to any siNA sequence targeting any chosen RNA and used, for example, in target screening assays to pick lead siNA compounds for therapeutic development (see for example FIG. 11).

Example 5 Chemical Synthesis and Purification of siNA

siNA molecules can be designed to interact with various sites in the RNA message, for example, target sequences within the RNA sequences described herein. The sequence of one strand of the siNA molecule(s) is complementary to the target site sequences described above. The siNA molecules can be chemically synthesized using methods described herein. Inactive siNA molecules that are used as control sequences can be synthesized by scrambling the sequence of the siNA molecules such that it is not complementary to the target sequence. Generally, siNA constructs can by synthesized using solid phase oligonucleotide synthesis methods as described herein (see for example Usman et al., U.S. Pat. Nos. 5,804,683; 5,831,071; 5,998,203; 6,117,657; 6,353,098; 6,362,323; 6,437,117; 6,469,158; Scaringe et al., U.S. Pat. Nos. 6,111,086; 6,008,400; 6,111,086 all incorporated by reference herein in their entirety).

In a non-limiting example, RNA oligonucleotides are synthesized in a stepwise fashion using the phosphoramidite chemistry as is known in the art. Standard phosphoramidite chemistry involves the use of nucleosides comprising any of 5′-O-dimethoxytrityl, 2′-O-tert-butyldimethylsilyl, 3′-O-2-Cyanoethyl N,N-diisopropylphosphoroamidite groups, and exocyclic amine protecting groups (e.g. N6-benzoyl adenosine, N4 acetyl cytidine, and N2-isobutyryl guanosine). Alternately, 2′-O-Silyl Ethers can be used in conjunction with acid-labile 2′-O-orthoester protecting groups in the synthesis of RNA as described by Scaringe supra. Differing 2′ chemistries can require different protecting groups, for example 2′-deoxy-2′-amino nucleosides can utilize N-phthaloyl protection as described by Usman et al., U.S. Pat. No. 5,631,360, incorporated by reference herein in its entirety).

During solid phase synthesis, each nucleotide is added sequentially (3′- to 5′-direction) to the solid support-bound oligonucleotide. The first nucleoside at the 3′-end of the chain is covalently attached to a solid support (e.g., controlled pore glass or polystyrene) using various linkers. The nucleotide precursor, a ribonucleoside phosphoramidite, and activator are combined resulting in the coupling of the second nucleoside phosphoramidite onto the 5′-end of the first nucleoside. The support is then washed and any unreacted 5′-hydroxyl groups are capped with a capping reagent such as acetic anhydride to yield inactive 5′-acetyl moieties. The trivalent phosphorus linkage is then oxidized to a more stable phosphate linkage. At the end of the nucleotide addition cycle, the 5′-O-protecting group is cleaved under suitable conditions (e.g., acidic conditions for trityl-based groups and Fluoride for silyl-based groups). The cycle is repeated for each subsequent nucleotide.

Modification of synthesis conditions can be used to optimize coupling efficiency, for example by using differing coupling times, differing reagent/phosphoramidite concentrations, differing contact times, differing solid supports and solid support linker chemistries depending on the particular chemical composition of the siNA to be synthesized. Deprotection and purification of the siNA can be performed as is generally described in Deprotection and purification of the siNA can be performed as is generally described in Usman et al., U.S. Pat. No. 5,831,071, U.S. Pat. No. 6,353,098, U.S. Pat. No. 6,437,117, and Bellon et al., U.S. Pat. No. 6,054,576, U.S. Pat. No. 6,162,909, U.S. Pat. No. 6,303,773, or Scaringe supra, incorporated by reference herein in their entireties. Additionally, deprotection conditions can be modified to provide the best possible yield and purity of siNA constructs. For example, applicant has observed that oligonucleotides comprising 2′-deoxy-2′-fluoro nucleotides can degrade under inappropriate deprotection conditions. Such oligonucleotides are deprotected using aqueous methylamine at about 35° C. for 30 minutes. If the 2′-deoxy-2′-fluoro containing oligonucleotide also comprises ribonucleotides, after deprotection with aqueous methylamine at about 35° C. for 30 minutes, TEA-HF is added and the reaction maintained at about 65° C. for an additional 15 minutes.

Example 6 RNAi In Vitro Assay to Assess siNA Activity

An in vitro assay that recapitulates RNAi in a cell-free system is used to evaluate siNA constructs targeting MAP kinase (e.g., c-JUN) RNA targets. The assay comprises the system described by Tuschl et al., 1999, Genes and Development, 13, 3191-3197 and Zamore et al., 2000, Cell, 101, 25-33 adapted for use with MAP kinase target RNA. A Drosophila extract derived from syncytial blastoderm is used to reconstitute RNAi activity in vitro. Target RNA is generated via in vitro transcription from an appropriate MAP kinase expressing plasmid using T7 RNA polymerase or via chemical synthesis as described herein. Sense and antisense siNA strands (for example 20 uM each) are annealed by incubation in buffer (such as 100 mM potassium acetate, 30 mM HEPES-KOH, pH 7.4, 2 mM magnesium acetate) for 1 minute at 90° C. followed by 1 hour at 37° C., then diluted in lysis buffer (for example 100 mM potassium acetate, 30 mM HEPES-KOH at pH 7.4, 2 mM magnesium acetate). Annealing can be monitored by gel electrophoresis on an agarose gel in TBE buffer and stained with ethidium bromide. The Drosophila lysate is prepared using zero to two-hour-old embryos from Oregon R flies collected on yeasted molasses agar that are dechorionated and lysed. The lysate is centrifuged and the supernatant isolated. The assay comprises a reaction mixture containing 50% lysate [vol/vol], RNA (10-50 μM final concentration), and 10% [vol/vol] lysis buffer containing siNA (10 nM final concentration). The reaction mixture also contains 10 mM creatine phosphate, 10 ug/ml creatine phosphokinase, 100 um GTP, 100 uM UTP, 100 uM CTP, 500 uM ATP, 5 mM DTT, 0.1 U/uL RNasin (Promega), and 100 uM of each amino acid. The final concentration of potassium acetate is adjusted to 100 mM. The reactions are pre-assembled on ice and preincubated at 25° C. for 10 minutes before adding RNA, then incubated at 25° C. for an additional 60 minutes. Reactions are quenched with 4 volumes of 1.25× Passive Lysis Buffer (Promega). Target RNA cleavage is assayed by RT-PCR analysis or other methods known in the art and are compared to control reactions in which siNA is omitted from the reaction.

Alternately, internally-labeled target RNA for the assay is prepared by in vitro transcription in the presence of [alpha-³²P] CTP, passed over a G 50 Sephadex column by spin chromatography and used as target RNA without further purification. Optionally, target RNA is 5′-³²P-end labeled using T4 polynucleotide kinase enzyme. Assays are performed as described above and target RNA and the specific RNA cleavage products generated by RNAi are visualized on an autoradiograph of a gel. The percentage of cleavage is determined by Phosphor Inager® quantitation of bands representing intact control RNA or RNA from control reactions without siNA and the cleavage products generated by the assay.

In one embodiment, this assay is used to determine target sites the MAP kinase RNA target for siNA mediated RNAi cleavage, wherein a plurality of siNA constructs are screened for RNAi mediated cleavage of the MAP kinase RNA target, for example, by analyzing the assay reaction by electrophoresis of labeled target RNA, or by northern blotting, as well as by other methodology well known in the art.

Example 7 Nucleic Acid Inhibition of MAP Kinase Target RNA In Vivo

siNA molecules targeted to the human MAP kinase (e.g., c-JUN) RNA are designed and synthesized as described above. These nucleic acid molecules can be tested for cleavage activity in vivo, for example, using the following procedure. The target sequences and the nucleotide location within the MAP kinase (e.g., c-JUN) RNA are given in Table II and III.

Two formats are used to test the efficacy of siNAs targeting MAP kinase (e.g., c-JUN). First, the reagents are tested in cell culture, for example using cultured human kidney fibroblast cells (e.g., 293, HeLa, or HepG2 cells), to determine the extent of RNA and protein inhibition. siNA reagents (e.g.; see Tables II and III) are selected against the MAP kinase (e.g., c-JUN) target as described herein. RNA inhibition is measured after delivery of these reagents by a suitable transfection agent to, for example, 293, HeLa, or HepG2 cells. Relative amounts of target RNA are measured versus actin using real-time PCR monitoring of amplification (eg., ABI 7700 Taqman®). A comparison is made to a mixture of oligonucleotide sequences made to unrelated targets or to a randomized siNA control with the same overall length and chemistry, but randomly substituted at each position. Primary and secondary lead reagents are chosen for the target and optimization performed. After an optimal transfection agent concentration is chosen, a RNA time-course of inhibition is performed with the lead siNA molecule. In addition, a cell-plating format can be used to determine RNA inhibition.

Delivery of siNA to Cells

Cells (e.g., 293, HeLa, or HepG2 cells) are seeded, for example, at 1×10⁵ cells per well of a six-well dish in EGM-2 (BioWhittaker) the day before transfection. siNA (final concentration, for example 20 nM) and cationic lipid (e.g., final concentration 2 μg/ml) are complexed in EGM basal media (BioWhittaker) at 37° C. for 30 mins in polystyrene tubes. Following vortexing, the complexed siNA is added to each well and incubated for the times indicated. For initial optimization experiments, cells are seeded, for example, at 1×10³ in 96 well plates and siNA complex added as described. Efficiency of delivery of siNA to cells is determined using a fluorescent siNA complexed with lipid. Cells in 6-well dishes are incubated with siNA for 24 hours, rinsed with PBS and fixed in 2% paraformaldehyde for 15 minutes at room temperature. Uptake of siNA is visualized using a fluorescent microscope.

Taqman and Lightcycler Quantification of mRNA

Total RNA is prepared from cells following siNA delivery, for example using Qiagen RNA purification kits for 6-well or Rneasy extraction kits for 96-well assays. For Taqman analysis, dual-labeled probes are synthesized with the reporter dye, FAM or JOE, covalently linked at the 5′-end and the quencher dye TAMRA conjugated to the 3′-end. One-step RT-PCR amplifications are performed on, for example, an ABI PRISM 7700 Sequence Detector using 50 μl reactions consisting of 10 μl total RNA, 100 nM forward primer, 900 nM reverse primer, 100 nM probe, 1×TaqMan PCR reaction buffer (PE-Applied Biosystems), 5.5 mM MgCl₂, 300 mM each dATP, dCTP, dGTP, and dTTP, 10U RNase Inhibitor (Promega), 1.25U AmpliTaq Gold (PE-Applied Biosystems) and 10U M-MLV Reverse Transcriptase (Promega). The thermal cycling conditions can consist of 30 min at 48° C., 10 min at 95° C., followed by 40 cycles of 15 sec at 95° C. and 1 min at 60° C. Quantitation of mRNA levels is determined relative to standards generated from serially diluted total cellular RNA (300, 100, 33, 11 ng/r×n) and normalizing to β-actin or GAPDH mRNA in parallel TaqMan reactions. For each gene of interest an upper and lower primer and a fluorescently labeled probe are designed. Real time incorporation of SYBR Green I dye into a specific PCR product can be measured in glass capillary tubes using a lightcyler. A standard curve is generated for each primer pair using control c RNA allularnd values are represented as relative expression to GAPDH in each sample.

Western Blotting

Nuclear extracts can be prepared using a standard micro preparation technique (see for example Andrews and Faller, 1991, Nucleic Acids Research, 19, 2499). Protein extracts from supernatants are prepared, for example using TCA precipitation. An equal volume of 20% TCA is added to the cell supernatant, incubated on ice for 1 hour and pelleted by centrifugation for 5 minutes. Pellets are washed in acetone, dried and resuspended in water. Cellular protein extracts are run on a 10% Bis-Tris NuPage (nuclear extracts) or 4-12% Tris-Glycine (supernatant extracts) polyacrylamide gel and transferred onto nitro-cellulose membranes. Non-specific binding can be blocked by incubation, for example, with 5% non-fat milk for 1 hour followed by primary antibody for 16 hour at 4° C. Following washes, the secondary antibody is applied, for example (1:10,000 dilution) for 1 hour at room temperature and the signal detected with SuperSignal reagent (Pierce).

Example 8 Models Useful to Evaluate the Down-Regulation of MAP Kinase Gene (e.g., c-JUN, ERK1, ERK2, JNK1, JNK2, and/or p38) expression Cell Culture

There are numerous cell culture systems that can be used to analyze reduction of MAP kinase levels either directly or indirectly by measuring downstream effects. For example, cultured human kidney fibroblast cells (e.g., 293 cells), HeLa, or HepG2 cells can be used in cell culture experiments to assess the efficacy of nucleic acid molecules of the invention. As such, cells treated with nucleic acid molecules of the invention (e.g., siNA) targeting MAP kinase RNA would be expected to have decreased MAP kinase expression capacity compared to matched control nucleic acid molecules having a scrambled or inactive sequence. In a non-limiting example, 293, HeLa, or HepG2 cells are cultured and MAP kinase expression is quantified, for example by time-resolved immuno fluorometric assay. MAP kinase messenger-RNA expression is quantitated with RT-PCR in cultured cells. Untreated cells are compared to cells treated with siNA molecules transfected with a suitable reagent, for example a cationic lipid such as lipofectamine, and MAP kinase protein and RNA levels are quantitated. Dose response assays are then performed to establish dose dependent inhibition of MAP kinase expression. In another non-limiting example, cell culture experiments are carried out as described by Aguirre et al., 2000, J. Biol. Chem., 275, 9047-9054.

In several cell culture systems, cationic lipids have been shown to enhance the bioavailability of oligonucleotides to cells in culture (Bennet, et al., 1992, Mol. Pharmacology, 41, 1023-1033). In one embodiment, siNA molecules of the invention are complexed with cationic lipids for cell culture experiments. siNA and cationic lipid mixtures are prepared in serum-free DMEM immediately prior to addition to the cells. DMEM plus additives are warmed to room temperature (about 20-25° C.) and cationic lipid is added to the final desired concentration and the solution is vortexed briefly. siNA molecules are added to the final desired concentration and the solution is again vortexed briefly and incubated for 10 minutes at room temperature. In dose response experiments, the RNA/lipid complex is serially diluted into DMEM following the 10 minute incubation.

Animal Models

Evaluating the efficacy of anti-MAP kinase agents in animal models is an important prerequisite to human clinical trials. Obesity and type 2 diabetes are the most prevalent and serious metabolic diseases in that they affect more than 50% of adults in the USA. These conditions are associated with a chronic inflammatory response characterized by abnormal inflammatory cytokine production, increased acute-phase reactants and other stress-induced molecules. Many of these alterations seem to be initiated and to reside within adipose tissue. Elevated production of tumor necrosis factor (TNF)-alpha by adipose tissue decreases sensitivity to insulin and has been detected in several experimental obesity models and obese humans. Free fatty acids (FFAs) are also implicated in the etiology of obesity-induced insulin resistance and diabetes. Because both TNF-alpha and FFAs are potent MAP kinase activators, Hirosumi et al., 2002, Nature, 420, 333-336 determined whether obesity is associated with alterations in stress-activated and inflammatory responses through this pathway and whether MAP kinases are causally linked to aberrant metabolic control in this state. In this study, Hirosumi et al., describe dietary and genetic (ob/ob) mouse models of obesity useful in evaluating MAP kinase gene expression. Such transgenic mice are useful as models for obesity and insulin resistance and can be used to identify nucleic acid molecules of the invention that modulate MAP kinase gene (e.g., ERK1, ERK2, JNK1, JNK2, and/or p38) expression and gene function toward therapeutic use in treating obesity and insulin resistance (e.g. type I and II diabetes).

The role of c-JUN in liver cancer has recently been investigated (Eferl et al., 2003, Cell, 112, 181). These investigators deleted c-JUN and then induced liver cancer by chemical carcinogenesis. They observed that deletion of c-JUN dramatically interfered with liver tumor formation. Animal survival was markedly worse in c-JUN wild-type animals relative to deletion mutants. In particular, the number of apoptotic cells increased about five fold in tumors in the c-JUN deletion strain relative to the wild-type animals. Importantly, levels of the pro-apoptotic gene products such as p53 and noxa were elevated in the c-JUN deletion strain. c-JUN is likely to antagonize other pro-apoptotic genes such as TNF-a. Thus, by blocking p53 and its large family of dependent genes, c-JUN seems to promote tumor formation. Since a large fraction of chronically infected HCV patients develop hepatocellular carcinoma, c-JUN provides an attractive target for treating HCV infected patients to prevent or ameliorate hepatocellular carcinoma. The animal model described by Eferl et al., supra, can be used to evaluate siNA molecules of the invention for efficacy in inhibiting c-JUN expression in liver toward therapeutic use in preventing and/or treating hepatocellular carcinoma in human subjects.

Because mitogen activated protein kinases (MAP kinases) are constituents of numerous signal transduction pathways, and are activated by protein kinase cascades, intense efforts are under way to develop and evaluate compounds that target components of MAPK pathways. Several of these inhibitors are effective in animal models of disease and have advanced to clinical trials for the treatment of inflammatory diseases, metabolic diseases, autoimmune diseases and cancer. The clinical utility of specifically targeting MAP kinase genes (e.g., c-JUN, ERK1, ERK2, JNK1, JNK2, and/or p38) can be studied in animal models and clinical studies of inflammatory diseases, metabolic diseases, autoimmune diseases and cancer (see for example English et al., 2002, Trends in Pharmacological Sciences, 23, 40-45).

Example 9 RNAi Mediated Inhibition of p38 RNA Expression

siNA constructs are tested for efficacy in reducing p38 RNA expression in, for example in A549 cells. Cells are plated approximately 24 hours before transfection in 96-well plates at 5,000-7,500 cells/well, 100 μl/well, such that at the time of transfection cells are 70-90% confluent. For transfection, annealed siNAs are mixed with the transfection reagent (Lipofectamine 2000, Invitrogen) in a volume of 50 μl/well and incubated for 20 minutes at room temperature. The siNA transfection mixtures are added to cells to give a final siNA concentration of 25 nM in a volume of 150 μl. Each siNA transfection mixture is added to 3 wells for triplicate siNA treatments. Cells are incubated at 37° for 24 hours in the continued presence of the siNA transfection mixture. At 24 hours, RNA is prepared from each well of treated cells. The supernatants with the transfection mixtures are first removed and discarded, then the cells are lysed and RNA prepared from each well. Target gene expression following treatment is evaluated by RT-PCR for the target gene and for a control gene (36B4, an RNA polymerase subunit) for normalization. The triplicate data is averaged and the standard deviations determined for each treatment. Normalized data are graphed and the percent reduction of target mRNA by active siNAs in comparison to their respective inverted control siNAs was determined.

In a non-limiting example, siNA constructs were screened for activity (see FIG. 12) and compared to untreated cells, scrambled siNA control constructs (Scram1 and Scram2), and cells transfected with lipid alone (transfection control). As shown in FIG. 12, the siNA constructs significantly reduce p38 RNA expression. Leads generated from such a screen are then further assayed. In a non-limiting example, siNA constructs comprising chemical modifications described herein (e.g., having modifications comprising Formulae I-VII and/or those modifications described in Table IV are assayed for activity. These siNA constructs are compared to appropriate matched chemistry inverted controls. In addition, the siNA constructs are also compared to untreated cells, cells transfected with lipid and scrambled siNA constructs, and cells transfected with lipid alone (transfection control).

Example 10 RNAi Mediated Inhibition of p38 RNA Expression

siNA constructs are tested for efficacy in reducing JNK1 RNA expression in, for example in A549 cells. Cells are plated approximately 24 hours before transfection in 96-well plates at 5,000-7,500 cells/well, 100 μl/well, such that at the time of transfection cells are 70-90% confluent. For transfection, annealed siNAs are mixed with the transfection reagent (Lipofectamine 2000, Invitrogen) in a volume of 50 μl/well and incubated for 20 minutes at room temperature. The siNA transfection mixtures are added to cells to give a final siNA concentration of 25 nM in a volume of 150 μl. Each siNA transfection mixture is added to 3 wells for triplicate siNA treatments. Cells are incubated at 37° for 24 hours in the continued presence of the siNA transfection mixture. At 24 hours, RNA is prepared from each well of treated cells. The supernatants with the transfection mixtures are first removed and discarded, then the cells are lysed and RNA prepared from each well. Target gene expression following treatment is evaluated by RT-PCR for the target gene and for a control gene (36B4, an RNA polymerase subunit) for normalization. The triplicate data is averaged and the standard deviations determined for each treatment. Normalized data are graphed and the percent reduction of target mRNA by active siNAs in comparison to their respective inverted control siNAs was determined.

In a non-limiting example, siNA constructs were screened for activity (see FIG. 13) and compared to untreated cells, scrambled siNA control constructs (Scram1 and Scram2), and cells transfected with lipid alone (transfection control). As shown in FIG. 13, the siNA constructs significantly reduce p38 RNA expression. Leads generated from such a screen are then further assayed. In a non-limiting example, siNA constructs comprise chemical modifications described herein (e.g., having modifications comprising Formulae I-VII and/or those modifications described in Table IV are assayed for activity). These siNA constructs are compared to appropriate matched chemistry inverted controls. In addition, the siNA constructs are also compared to untreated cells, cells transfected with lipid and scrambled siNA constructs, and cells transfected with lipid alone (transfection control).

Example 11 Indications

The present body of knowledge in MAP kinase research indicates the need for methods and compounds that can regulate MAP kinase gene (e.g., c-JUN, ERK1, ERK2, JNK1, JNK2, and/or p38) product expression for research, diagnostic, and therapeutic use. As described herein, the nucleic acid molecules of the present invention can be used to treat obesity and insulin resistance (e.g. type I and II diabetes), oncology and proliferation related indications and conditions, including cancers of the lung, bladder, colon, breast, prostate, retina, larynx, esophagus, liver (e.g., hepatocellular carcinoma), and ovary, along with lymphomas, melanomas and glioblastomas, inflammatory disorders such as asthma, septic shock, rheumatoid arthritis, psoriasis, inflammatory bowl syndrome and any other disease that responds to modulation of MAP kinase expression.

Troglitazone, insulin, and PTP-1B modulators are non-limiting examples of pharmaceutical agents that can be combined with or used in conjunction with the nucleic acid molecules (e.g. siNA molecules) of the instant invention for treating obesity and diabetes. The use of radiation treatments and chemotherapeutics such as Gemcytabine and cyclophosphamide are non-limiting examples of chemotherapeutic agents that can also be combined with or used in conjunction with the nucleic acid molecules (e.g. siNA molecules) of the instant invention for oncology therapeutic applications. Those skilled in the art will recognize that other anti-cancer compounds and therapies can be similarly be readily combined with the nucleic acid molecules of the instant invention (e.g. siNA molecules) and are hence within the scope of the instant invention. Such compounds and therapies are well known in the art (see for example Cancer: Principles and Practice of Oncology, Volumes 1 and 2, eds Devita, V. T., Hellman, S., and Rosenberg, S. A., J.B. Lippincott Company, Philadelphia, USA; incorporated herein by reference) and include, without limitations, folates, antifolates, pyrimidine analogs, fluoropyrimidines, purine analogs, adenosine analogs, topoisomerase I inhibitors, anthrapyrazoles, retinoids, antibiotics, anthacyclins, platinum analogs, alkylating agents, nitrosoureas, plant derived compounds such as vinca alkaloids, epipodophyllotoxins, tyrosine kinase inhibitors, taxols, radiation therapy, surgery, nutritional supplements, gene therapy, radiotherapy, for example 3D-CRT, immunotoxin therapy, for example ricin, and monoclonal antibodies. Specific examples of chemotherapeutic compounds that can be combined with or used in conjunction with the nucleic acid molecules of the invention include, but are not limited to, Paclitaxel; Docetaxel; Methotrexate; Doxorubin; Edatrexate; Vinorelbine; Tamoxifen; Leucovorin; 5-fluoro uridine (5-FU); Ionotecan; Cisplatin; Carboplatin; Amsacrine; Cytarabine; Bleomycin; Mitomycin C; Dactinomycin; Mithramycin; Hexamethylmelamine; Dacarbazine; L-asperginase; Nitrogen mustard; Melphalan, Chlorambucil; Busulfan; Ifosfamide; 4-hydroperoxycyclophosphamide, Thiotepa; Irinotecan (CAMPTOSAR®, CPT-11, Camptothecin-11, Campto) Tamoxifen, Herceptin; IMC C225; ABX-EGF: and combinations thereof are non-limiting examples of compounds and/or methods that can be combined with or used in conjunction with the nucleic acid molecules (e.g. siNA) of the instant invention. In addition, treatment of HCV infected subjects with siNA molecules of the invention targeting c-JUN or other MAP kinases involved in the maintenance or development of hepatocellular carcinoma can be combined with anti-viral compounds, such as siNA molecules targeting HCV RNA or other antiviral compounds known in the art (e.g., interferons, nucleoside analogs etc.). Those skilled in the art will recognize that other drug compounds and therapies can be similarly be readily combined with the nucleic acid molecules of the instant invention (e.g., siNA molecules) are hence within the scope of the instant invention.

Example 12 Diagnostic Uses

The siNA molecules of the invention can be used in a variety of diagnostic applications, such as in the identification of molecular targets (e.g., RNA) in a variety of applications, for example, in clinical, industrial, environmental, agricultural and/or research settings. Such diagnostic use of siNA molecules involves utilizing reconstituted RNAi systems, for example, using cellular lysates or partially purified cellular lysates. siNA molecules of this invention can be used as diagnostic tools to examine genetic drift and mutations within diseased cells or to detect the presence of endogenous or exogenous, for example viral, RNA in a cell. The close relationship between siNA activity and the structure of the target RNA allows the detection of mutations in any region of the molecule, which alters the base-pairing and three-dimensional structure of the target RNA. By using multiple siNA molecules described in this invention, one ca MAP nucleotide changes, which are important to RNA structure and function in vitro, as well as in cells and tissues. Cleavage of target RNAs with siNA molecules can be used to inhibit gene expression and define the role of specified gene products in the progression of disease or infection. In this manner, other genetic targets can be defined as important mediators of the disease. These experiments will lead to better treatment of the disease progression by affording the possibility of combination therapies (e.g., multiple siNA molecules targeted to different genes, siNA molecules coupled with known small molecule inhibitors, or intermittent treatment with combinations siNA molecules and/or other chemical or biological molecules). Other in vitro uses of siNA molecules of this invention are well known in the art, and include detection of the presence of mRNAs associated with a disease, infection, or related condition. Such RNA is detected by determining the presence of a cleavage product after treatment with a siNA using standard methodologies, for example, fluorescence resonance emission transfer (FRET).

In a specific example, siNA molecules that cleave only wild-type or mutant forms of the target RNA are used for the assay. The first siNA molecules (i.e., those that cleave only wild-type forms of target RNA) are used to identify wild-type RNA present in the sample and the second siNA molecules (i.e., those that cleave only mutant forms of target RNA) are used to identify mutant RNA in the sample. As reaction controls, synthetic substrates of both wild-type and mutant RNA are cleaved by both siNA molecules to demonstrate the relative siNA efficiencies in the reactions and the absence of cleavage of the “non-targeted” RNA species. The cleavage products from the synthetic substrates also serve to generate size markers for the analysis of wild-type and mutant RNAs in the sample population. Thus, each analysis requires two siNA molecules, two substrates and one unknown sample, which is combined into six reactions. The presence of cleavage products is determined using an RNase protection assay so that full-length and cleavage fragments of each RNA can be analyzed in one lane of a polyacrylamide gel. It is not absolutely required to quantify the results to gain insight into the expression of mutant RNAs and putative risk of the desired phenotypic changes in target cells. The expression of mRNA whose protein product is implicated in the development of the phenotype (i.e., disease related or infection related) is adequate to establish risk. If probes of comparable specific activity are used for both transcripts, then a qualitative comparison of RNA levels is adequate and decreases the cost of the initial diagnosis. Higher mutant form to wild-type ratios are correlated with higher risk whether RNA levels are compared qualitatively or quantitatively.

All patents and publications mentioned in the specification are indicative of the levels of skill of those skilled in the art to which the invention pertains. All references cited in this disclosure are incorporated by reference to the same extent as if each reference had been incorporated by reference in its entirety individually.

One skilled in the art would readily appreciate that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. The methods and compositions described herein as presently representative of preferred embodiments are exemplary and are not intended as limitations on the scope of the invention. Changes therein and other uses will occur to those skilled in the art, which are encompassed within the spirit of the invention, are defined by the scope of the claims.

It will be readily apparent to one skilled in the art that varying substitutions and modifications can be made to the invention disclosed herein without departing from the scope and spirit of the invention. Thus, such additional embodiments are within the scope of the present invention and the following claims. The present invention teaches one skilled in the art to test various combinations and/or substitutions of chemical modifications described herein toward generating nucleic acid constructs with improved activity for mediating RNAi activity. Such improved activity can comprise improved stability, improved bioavailability, and/or improved activation of cellular responses mediating RNAi. Therefore, the specific embodiments described herein are not limiting and one skilled in the art can readily appreciate that specific combinations of the modifications described herein can be tested without undue experimentation toward identifying siNA molecules with improved RNAi activity.

The invention illustratively described herein suitably can be practiced in the absence of any element or elements, limitation or limitations that are not specifically disclosed herein. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention that in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by preferred embodiments, optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the description and the appended claims.

In addition, where features or aspects of the invention are described in terms of Markush groups or other grouping of alternatives, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group or other group.

TABLE I MAP kinase Accession Numbers NM_002745 Homo sapiens mitogen-activated protein kinase 1 (MAPK1), transcript variant 1, mRNA. NM_138957 Homo sapiens mitogen-activated protein kinase 1 (MAPK1), transcript variant 2, mRNA. X60188 Human ERK1 mRNA for protein serine/threonine kinase (MAPK3). XM_055766 Homo sapiens mitogen-activated protein kinase 3 (MAPK3), mRNA NM_002747 Homo sapiens mitogen-activated protein kinase 4 (MAPK4), mRNA XM_165662 Homo sapiens Mitogen-activated protein kinase 4 (Extracellular signal-regulated kinase 4) (ERK-4) (MAP kinase isoform p63) (p63-MAPK) (LOC220131), mRNA NM_002748 Homo sapiens mitogen-activated protein kinase 6 (MAPK6), mRNA. XM_166057 Homo sapiens Mitogen-activated protein kinase 6 (Extracellular signal-regulated kinase 3) (ERK-3) (MAP kinase isoform p97) (p97-MAPK) (LOC220839), mRNA XM_035575 Homo sapiens mitogen-activated protein kinase 6 (MAPK6), mRNA NM_139033 Homo sapiens mitogen-activated protein kinase 7 (MAPK7), transcript variant 1, mRNA NM_139032 Homo sapiens mitogen-activated protein kinase 7 (MAPK7), transcript variant 2, mRNA NM_002749 Homo sapiens mitogen-activated protein kinase 7 (MAPK7), transcript variant 3, mRNA NM_139034 Homo sapiens mitogen-activated protein kinase 7 (MAPK7), transcript variant 4, mRNA NM_139049 Homo sapiens mitogen-activated protein kinase 8 (MAPK8), transcript variant 1, mRNA. NM_002750 Homo sapiens mitogen-activated protein kinase 8 (MAPK8), transcript variant 2, mRNA. NM_139046 Homo sapiens mitogen-activated protein kinase 8 (MAPK8), transcript variant 3, mRNA. NM_139047 Homo sapiens mitogen-activated protein kinase 8 (MAPK8), transcript variant 4, mRNA. NM_002752 Homo sapiens mitogen-activated protein kinase 9 (MAPK9), transcript variant 1, mRNA. NM_139068 Homo sapiens mitogen-activated protein kinase 9 (MAPK9), transcript variant 2, mRNA. NM_139069 Homo sapiens mitogen-activated protein kinase 9 (MAPK9), transcript variant 3, mRNA. NM_139070 Homo sapiens mitogen-activated protein kinase 9 (MAPK9), transcript variant 4, mRNA. NM_002753 Homo sapiens mitogen-activated protein kinase 10 (MAPK10), transcript variant 1, mRNA NM_138982 Homo sapiens mitogen-activated protein kinase 10 (MAPK10), transcript variant 2, mRNA NM_138980 Homo sapiens mitogen-activated protein kinase 10 (MAPK10), transcript variant 3, mRNA NM_138981 Homo sapiens mitogen-activated protein kinase 10 (MAPK10), transcript variant 4, mRNA NM_002751 Homo sapiens mitogen-activated protein kinase 11 (MAPK11), transcript variant 1, mRNA. NM_138993 Homo sapiens mitogen-activated protein kinase 11 (MAPK11), transcript variant 2, mRNA. NM_002969 Homo sapiens mitogen-activated protein kinase 12 (MAPK12), mRNA. NM_002754 Homo sapiens mitogen-activated protein kinase 13 (MAPK13), mRNA. NM_001315 Homo sapiens mitogen-activated protein kinase 14 (MAPK14), transcript variant 1, mRNA. NM_139012 Homo sapiens mitogen-activated protein kinase 14 (MAPK14), transcript variant 2, mRNA. NM_139013 Homo sapiens mitogen-activated protein kinase 14 (MAPK14), transcript variant 3, mRNA. NM_139014 Homo sapiens mitogen-activated protein kinase 14 (MAPK14), transcript variant 4, mRNA. NM_002755 Homo sapiens mitogen-activated protein kinase kinase 1 (MAP2K1), mRNA NM_030662 Homo sapiens mitogen-activated protein kinase kinase 2 (MAP2K2), mRNA NM_002756 Homo sapiens mitogen-activated protein kinase kinase 3 (MAP2K3), transcript variant A, mRNA NM_145109 Homo sapiens mitogen-activated protein kinase kinase 3 (MAP2K3), transcript variant B, mRNA NM_145110 Homo sapiens mitogen-activated protein kinase kinase 3 (MAP2K3), transcript variant C, mRNA XM_008654 Homo sapiens mitogen-activated protein kinase kinase 4 (MAP2K4), mRNA NM_003010 Homo sapiens mitogen-activated protein kinase kinase 4 (MAP2K4), mRNA NM_145160 Homo sapiens mitogen-activated protein kinase kinase 5 (MAP2K5), transcript variant A, mRNA NM_002757 Homo sapiens mitogen-activated protein kinase kinase 5 (MAP2K5), transcript variant B, mRNA NM_145161 Homo sapiens mitogen-activated protein kinase kinase 5 (MAP2K5), transcript variant C, mRNA NM_145162 Homo sapiens mitogen-activated protein kinase kinase 5 (MAP2K5), transcript variant D, mRNA XM_113313 Homo sapiens mitogen-activated protein kinase kinase 6 (MAP2K6), mRNA NM_002758 Homo sapiens mitogen-activated protein kinase kinase 6 (MAP2K6), transcript variant 1, mRNA NM_031988 Homo sapiens mitogen-activated protein kinase kinase 6 (MAP2K6), transcript variant 2, mRNA NM_005043 Homo sapiens mitogen-activated protein kinase kinase 7 (MAP2K7), transcript variant A, mRNA NM_145185 Homo sapiens mitogen-activated protein kinase kinase 7 (MAP2K7), transcript variant B, mRNA NM_145329 Homo sapiens mitogen-activated protein kinase kinase 7 (MAP2K7), transcript variant C, mRNA AF042838 Homo sapiens mitogen-activated protein kinase kinase kinase 1 (MAP3K1), mRNA NM_006609 Homo sapiens mitogen-activated protein kinase kinase kinase 2 (MAP3K2), mRNA NM_002401 Homo sapiens mitogen-activated protein kinase kinase kinase 3 (MAP3K3), mRNA NM_005922 Homo sapiens mitogen-activated protein kinase kinase kinase 4 (MAP3K4), transcript variant 1, mRNA NM_006724 Homo sapiens mitogen-activated protein kinase kinase kinase 4 (MAP3K4), transcript variant 2, mRNA NM_005923 Homo sapiens mitogen-activated protein kinase kinase kinase 5 (MAP3K5), mRNA NM_004672 Homo sapiens mitogen-activated protein kinase kinase kinase 6 (MAP3K6), mRNA NM_003188 Homo sapiens mitogen-activated protein kinase kinase kinase 7 (MAP3K7), mRNA NM_005204 Homo sapiens mitogen-activated protein kinase kinase kinase 8 (MAP3K8), mRNA AF251442 Homo sapiens mitogen-activated protein kinase kinase kinase 9 (MAP3K9), mRNA NM_002446 Homo sapiens mitogen-activated protein kinase kinase kinase 10 (MAP3K10), mRNA NM_002419 Homo sapiens mitogen-activated protein kinase kinase kinase 11 (MAP3K11), mRNA NM_006301 Homo sapiens mitogen-activated protein kinase kinase kinase 12 (MAP3K12), mRNA NM_004721 Homo sapiens mitogen-activated protein kinase kinase kinase 13 (MAP3K13), mRNA NM_003954 Homo sapiens mitogen-activated protein kinase kinase kinase 14 (MAP3K14), mRNA NM_007181 Homo sapiens mitogen-activated protein kinase kinase kinase kinase 1 (MAP4K1), mRNA NM_004579 Homo sapiens mitogen-activated protein kinase kinase kinase kinase 2 (MAP4K2), mRNA NM_003618 Homo sapiens mitogen-activated protein kinase kinase kinase kinase 3 (MAP4K3), mRNA NM_004834 Homo sapiens mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4), mRNA NM_006575 Homo sapiens mitogen-activated protein kinase kinase kinase kinase 5 (MAP4K5), mRNA NM_003668 Homo sapiens mitogen-activated protein kinase-activated protein kinase 5 (MAPKAPK5), transcript variant 1, mRNA NM_139078 Homo sapiens mitogen-activated protein kinase-activated protein kinase 5 (MAPKAPK5), transcript variant 2, mRNA NM_004635 Homo sapiens mitogen-activated protein kinase-activated protein kinase 3 (MAPKAPK3), mRNA NM_004759 Homo sapiens mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2), transcript variant 1, mRNA NM_032960 Homo sapiens mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2), transcript variant 2, mRNA NM_005373 Homo sapiens myeloproliferative leukemia virus oncogene (MPL), mRNA NM_016848 Homo sapiens neuronal Shc (SHC3), mRNA NM_002649 Homo sapiens phosphoinositide-3-kinase, catalytic, gamma polypeptide (PIK3CG), mRNA NM_021003 Homo sapiens protein phosphatase 1A (formerly 2C), magnesium-dependent, alpha isoform (PPM1A), mRNA NM_003942 Homo sapiens ribosomal protein S6 kinase, 90 kD, polypeptide 4 (RPS6KA4), mRNA NM_004755 Homo sapiens ribosomal protein S6 kinase, 90 kD, polypeptide 5 (RPS6KA5), mRNA NM_002228 Homo sapiens v-jun sarcoma virus 17 oncogene homolog (avian) (JUN), mRNA

TABLE II MAP kinase siNA and Target Sequences Seq Seq Seq Pos Target Sequence ID UPos Upper seq ID LPos Lower seq ID NM_002745 (MAPK1/ERK2) 3 CCCUCCCUCCGCCCGCCCG 1 3 CCCUCCCUCCGCCCGCCCG 1 21 CGGGCGGGCGGAGGGAGGG 164 21 GCCGGCCCGCCCGUCAGUC 2 21 GCCGGCCCGCCCGUCAGUC 2 39 GACUGACGGGCGGGCCGGC 165 39 CUGGCAGGCAGGCAGGCAA 3 39 CUGGCAGGCAGGCAGGCAA 3 57 UUGCCUGCCUGCCUGCCAG 166 57 AUCGGUCCGAGUGGCUGUC 4 57 AUCGGUCCGAGUGGCUGUC 4 75 GACAGCCACUCGGACCGAU 167 75 CGGCUCUUCAGCUCUCCCG 5 75 CGGCUCUUCAGCUCUCCCG 5 93 CGGGAGAGCUGAAGAGCCG 168 93 GCUCGGCGUCUUCCUUCCU 6 93 GCUCGGCGUCUUCCUUCCU 6 111 AGGAAGGAAGACGCCGAGC 169 111 UCCUCCCGGUCAGCGUCGG 7 111 UCCUCCCGGUCAGCGUCGG 7 129 CCGACGCUGACCGGGAGGA 170 129 GCGGCUGCACCGGCGGCGG 8 129 GCGGCUGCACCGGCGGCGG 8 147 CCGCCGCCGGUGCAGCCGC 171 147 GCGCAGUCCCUGCGGGAGG 9 147 GCGCAGUCCCUGCGGGAGG 9 165 CCUCCCGCAGGGACUGCGC 172 165 GGGCGACAAGAGCUGAGCG 10 165 GGGCGACAAGAGCUGAGCG 10 183 CGCUCAGCUCUUGUCGCCC 173 183 GGCGGCCGCCGAGCGUCGA 11 183 GGCGGCCGCCGAGCGUCGA 11 201 UCGACGCUCGGCGGCCGCC 174 201 AGCUCAGCGCGGCGGAGGC 12 201 AGCUCAGCGCGGCGGAGGC 12 219 GCCUCCGCCGCGCUGAGCU 175 219 CGGCGGCGGCCCGGCAGCC 13 219 CGGCGGCGGCCCGGCAGCC 13 237 GGCUGCCGGGCCGCCGCCG 176 237 CAACAUGGCGGCGGCGGCG 14 237 CAACAUGGCGGCGGCGGCG 14 255 CGCCGCCGCCGCCAUGUUG 177 255 GGCGGCGGGCGCGGGCCCG 15 255 GGCGGCGGGCGCGGGCCCG 15 273 CGGGCCCGCGCCCGCCGCC 178 273 GGAGAUGGUCCGCGGGCAG 16 273 GGAGAUGGUCCGCGGGCAG 16 291 CUGCCCGCGGACCAUCUCC 179 291 GGUGUUCGACGUGGGGCCG 17 291 GGUGUUCGACGUGGGGCCG 17 309 CGGCCCCACGUCGAACACC 180 309 GCGCUACACCAACCUCUCG 18 309 GCGCUACACCAACCUCUCG 18 327 CGAGAGGUUGGUGUAGCGC 181 327 GUACAUCGGCGAGGGCGCC 19 327 GUACAUCGGCGAGGGCGCC 19 345 GGCGCCCUCGCCGAUGUAC 182 345 CUACGGCAUGGUGUGCUCU 20 345 CUACGGCAUGGUGUGCUCU 20 363 AGAGCACACCAUGCCGUAG 183 363 UGCUUAUGAUAAUGUCAAC 21 363 UGCUUAUGAUAAUGUCAAC 21 381 GUUGACAUUAUCAUAAGCA 184 381 CAAAGUUCGAGUAGCUAUC 22 381 CAAAGUUCGAGUAGCUAUC 22 399 GAUAGCUACUCGAACUUUG 185 399 CAAGAAAAUCAGCCCCUUU 23 399 CAAGAAAAUCAGCCCCUUU 23 417 AAAGGGGCUGAUUUUCUUG 186 417 UGAGCACCAGACCUACUGC 24 417 UGAGCACCAGACCUACUGC 24 435 GCAGUAGGUCUGGUGCUCA 187 435 CCAGAGAACCCUGAGGGAG 25 435 CCAGAGAACCCUGAGGGAG 25 453 CUCCCUCAGGGUUCUCUGG 188 453 GAUAAAAAUCUUACUGCGC 26 453 GAUAAAAAUCUUACUGCGC 26 471 GCGCAGUAAGAUUUUUAUC 189 471 CUUCAGACAUGAGAACAUC 27 471 CUUCAGACAUGAGAACAUC 27 489 GAUGUUCUCAUGUCUGAAG 190 489 CAUUGGAAUCAAUGACAUU 28 489 CAUUGGAAUCAAUGACAUU 28 507 AAUGUCAUUGAUUCCAAUG 191 507 UAUUCGAGCACCAACCAUC 29 507 UAUUCGAGCACCAACCAUC 29 525 GAUGGUUGGUGCUCGAAUA 192 525 CGAGCAAAUGAAAGAUGUA 30 525 CGAGCAAAUGAAAGAUGUA 30 543 UACAUCUUUCAUUUGCUCG 193 543 AUAUAUAGUACAGGACCUC 31 543 AUAUAUAGUACAGGACCUC 31 561 GAGGUCCUGUACUAUAUAU 194 561 CAUGGAAACAGAUCUUUAC 32 561 CAUGGAAACAGAUCUUUAC 32 579 GUAAAGAUCUGUUUCCAUG 195 579 CAAGCUCUUGAAGACACAA 33 579 CAAGCUCUUGAAGACACAA 33 597 UUGUGUCUUCAAGAGCUUG 196 597 ACACCUCAGCAAUGACCAU 34 597 ACACCUCAGCAAUGACCAU 34 615 AUGGUCAUUGCUGAGGUGU 197 615 UAUCUGCUAUUUUCUCUAC 35 615 UAUCUGCUAUUUUCUCUAC 35 633 GUAGAGAAAAUAGCAGAUA 198 633 CCAGAUCCUCAGAGGGUUA 36 633 CCAGAUCCUCAGAGGGUUA 36 651 UAACCCUCUGAGGAUCUGG 199 651 AAAAUAUAUCCAUUCAGCU 37 651 AAAAUAUAUCCAUUCAGCU 37 669 AGCUGAAUGGAUAUAUUUU 200 669 UAACGUUCUGCACCGUGAC 38 669 UAACGUUCUGCACCGUGAC 38 687 GUCACGGUGCAGAACGUUA 201 687 CCUCAAGCCUUCCAACCUG 39 687 CCUCAAGCCUUCCAACCUG 39 705 CAGGUUGGAAGGCUUGAGG 202 705 GCUGCUCAACACCACCUGU 40 705 GCUGCUCAACACCACCUGU 40 723 ACAGGUGGUGUUGAGCAGC 203 723 UGAUCUCAAGAUCUGUGAC 41 723 UGAUCUCAAGAUCUGUGAC 41 741 GUCACAGAUCUUGAGAUCA 204 741 CUUUGGCCUGGCCCGUGUU 42 741 CUUUGGCCUGGCCCGUGUU 42 759 AACACGGGCCAGGCCAAAG 205 759 UGCAGAUCCAGACCAUGAU 43 759 UGCAGAUCCAGACCAUGAU 43 777 AUCAUGGUCUGGAUCUGCA 206 777 UCACACAGGGUUCCUGACA 44 777 UCACACAGGGUUCCUGACA 44 795 UGUCAGGAACCCUGUGUGA 207 795 AGAAUAUGUGGCCACACGU 45 795 AGAAUAUGUGGCCACACGU 45 813 ACGUGUGGCCACAUAUUCU 208 813 UUGGUACAGGGCUCCAGAA 46 813 UUGGUACAGGGCUCCAGAA 46 831 UUCUGGAGCCCUGUACCAA 209 831 AAUUAUGUUGAAUUCCAAG 47 831 AAUUAUGUUGAAUUCCAAG 47 849 CUUGGAAUUCAACAUAAUU 210 849 GGGCUACACCAAGUCCAUU 48 849 GGGCUACACCAAGUCCAUU 48 867 AAUGGACUUGGUGUAGCCC 211 867 UGAUAUUUGGUCUGUAGGC 49 867 UGAUAUUUGGUCUGUAGGC 49 885 GCCUACAGACCAAAUAUCA 212 885 CUGCAUUCUGGCAGAAAUG 50 885 CUGCAUUCUGGCAGAAAUG 50 903 CAUUUCUGCCAGAAUGCAG 213 903 GCUUUCUAACAGGCCCAUC 51 903 GCUUUCUAACAGGCCCAUC 51 921 GAUGGGCCUGUUAGAAAGC 214 921 CUUUCCAGGGAAGCAUUAU 52 921 CUUUCCAGGGAAGCAUUAU 52 939 AUAAUGCUUCCCUGGAAAG 215 939 UCUUGACCAGCUGAAACAC 53 939 UCUUGACCAGCUGAAACAC 53 957 GUGUUUCAGCUGGUCAAGA 216 957 CAUUUUGGGUAUUCUUGGA 54 957 CAUUUUGGGUAUUCUUGGA 54 975 UCCAAGAAUACCCAAAAUG 217 975 AUCCCCAUCACAAGAAGAC 55 975 AUCCCCAUCACAAGAAGAC 55 993 GUCUUCUUGUGAUGGGGAU 218 993 CCUGAAUUGUAUAAUAAAU 56 993 CCUGAAUUGUAUAAUAAAU 56 1011 AUUUAUUAUACAAUUCAGG 219 1011 UUUAAAAGCUAGGAACUAU 57 1011 UUUAAAAGCUAGGAACUAU 57 1029 AUAGUUCCUAGCUUUUAAA 220 1029 UUUGCUUUCUCUUCCACAC 58 1029 UUUGCUUUCUCUUCCACAC 58 1047 GUGUGGAAGAGAAAGCAAA 221 1047 CAAAAAUAAGGUGCCAUGG 59 1047 CAAAAAUAAGGUGCCAUGG 59 1065 CCAUGGCACCUUAUUUUUG 222 1065 GAACAGGCUGUUCCCAAAU 60 1065 GAACAGGCUGUUCCCAAAU 60 1083 AUUUGGGAACAGCCUGUUC 223 1083 UGCUGACUCCAAAGCUCUG 61 1083 UGCUGACUCCAAAGCUCUG 61 1101 CAGAGCUUUGGAGUCAGCA 224 1101 GGACUUAUUGGACAAAAUG 62 1101 GGACUUAUUGGACAAAAUG 62 1119 CAUUUUGUCCAAUAAGUCC 225 1119 GUUGACAUUCAACCCACAC 63 1119 GUUGACAUUCAACCCACAC 63 1137 GUGUGGGUUGAAUGUCAAC 226 1137 CAAGAGGAUUGAAGUAGAA 64 1137 CAAGAGGAUUGAAGUAGAA 64 1155 UUCUACUUCAAUCCUCUUG 227 1155 ACAGGCUCUGGCCCACCCA 65 1155 ACAGGCUCUGGCCCACCCA 65 1173 UGGGUGGGCCAGAGCCUGU 228 1173 AUAUCUGGAGCAGUAUUAC 66 1173 AUAUCUGGAGCAGUAUUAC 66 1191 GUAAUACUGCUCCAGAUAU 229 1191 CGACCCGAGUGACGAGCCC 67 1191 CGACCCGAGUGACGAGCCC 67 1209 GGGCUCGUCACUCGGGUCG 230 1209 CAUCGCCGAAGCACCAUUC 68 1209 CAUCGCCGAAGCACCAUUC 68 1227 GAAUGGUGCUUCGGCGAUG 231 1227 CAAGUUCGACAUGGAAUUG 69 1227 CAAGUUCGACAUGGAAUUG 69 1245 CAAUUCCAUGUCGAACUUG 232 1245 GGAUGACUUGCCUAAGGAA 70 1245 GGAUGACUUGCCUAAGGAA 70 1263 UUCCUUAGGCAAGUCAUCC 233 1263 AAAGCUCAAAGAACUAAUU 71 1263 AAAGCUCAAAGAACUAAUU 71 1281 AAUUAGUUCUUUGAGCUUU 234 1281 UUUUGAAGAGACUGCUAGA 72 1281 UUUUGAAGAGACUGCUAGA 72 1299 UCUAGCAGUCUCUUCAAAA 235 1299 AUUCCAGCCAGGAUACAGA 73 1299 AUUCCAGCCAGGAUACAGA 73 1317 UCUGUAUCCUGGCUGGAAU 236 1317 AUCUUAAAUUUGUCAGGAC 74 1317 AUCUUAAAUUUGUCAGGAC 74 1335 GUCCUGACAAAUUUAAGAU 237 1335 CAAGGGCUCAGAGGACUGG 75 1335 CAAGGGCUCAGAGGACUGG 75 1353 CCAGUCCUCUGAGCCCUUG 238 1353 GACGUGCUCAGACAUCGGU 76 1353 GACGUGCUCAGACAUCGGU 76 1371 ACCGAUGUCUGAGCACGUC 239 1371 UGUUCUUCUUCCCAGUUCU 77 1371 UGUUCUUCUUCCCAGUUCU 77 1389 AGAACUGGGAAGAAGAACA 240 1389 UUGACCCCUGGUCCUGUCU 78 1389 UUGACCCCUGGUCCUGUCU 78 1407 AGACAGGACCAGGGGUCAA 241 1407 UCCAGCCCGUCUUGGCUUA 79 1407 UCCAGCCCGUCUUGGCUUA 79 1425 UAAGCCAAGACGGGCUGGA 242 1425 AUCCACUUUGACUCCUUUG 80 1425 AUCCACUUUGACUCCUUUG 80 1443 CAAAGGAGUCAAAGUGGAU 243 1443 GAGCCGUUUGGAGGGGCGG 81 1443 GAGCCGUUUGGAGGGGCGG 81 1461 CCGCCCCUCCAAACGGCUC 244 1461 GUUUCUGGUAGUUGUGGCU 82 1461 GUUUCUGGUAGUUGUGGCU 82 1479 AGCCACAACUACCAGAAAC 245 1479 UUUUAUGCUUUCAAAGAAU 83 1479 UUUUAUGCUUUCAAAGAAU 83 1497 AUUCUUUGAAAGCAUAAAA 246 1497 UUUCUUCAGUCCAGAGAAU 84 1497 UUUCUUCAGUCCAGAGAAU 84 1515 AUUCUCUGGACUGAAGAAA 247 1515 UUCCUCCUGGCAGCCCUGU 85 1515 UUCCUCCUGGCAGCCCUGU 85 1533 ACAGGGCUGCCAGGAGGAA 248 1533 UGUGUGUCACCCAUUGGUG 86 1533 UGUGUGUCACCCAUUGGUG 86 1551 CACCAAUGGGUGACACACA 249 1551 GACCUGCGGCAGUAUGUAC 87 1551 GACCUGCGGCAGUAUGUAC 87 1569 GUACAUACUGCCGCAGGUC 250 1569 CUUCAGUGCACCUUACUGC 88 1569 CUUCAGUGCACCUUACUGC 88 1587 GCAGUAAGGUGCACUGAAG 251 1587 CUUACUGUUGCUUUAGUCA 89 1587 CUUACUGUUGCUUUAGUCA 89 1605 UGACUAAAGCAACAGUAAG 252 1605 ACUAAUUGCUUUCUGGUUU 90 1605 ACUAAUUGCUUUCUGGUUU 90 1623 AAACCAGAAAGCAAUUAGU 253 1623 UGAAAGAUGCAGUGGUUCC 91 1623 UGAAAGAUGCAGUGGUUCC 91 1641 GGAACCACUGCAUCUUUCA 254 1641 CUCCCUCUCCUGAAUCCUU 92 1641 CUCCCUCUCCUGAAUCCUU 92 1659 AAGGAUUCAGGAGAGGGAG 255 1659 UUUCUACAUGAUGCCCUGC 93 1659 UUUCUACAUGAUGCCCUGC 93 1677 GCAGGGCAUCAUGUAGAAA 256 1677 CUGACCAUGCAGCCGCACC 94 1677 CUGACCAUGCAGCCGCACC 94 1695 GGUGCGGCUGCAUGGUCAG 257 1695 CAGAGAGAGAUUCUUCCCC 95 1695 CAGAGAGAGAUUCUUCCCC 95 1713 GGGGAAGAAUCUCUCUCUG 258 1713 CAAUUGGCUCUAGUCACUG 96 1713 CAAUUGGCUCUAGUCACUG 96 1731 CAGUGACUAGAGCCAAUUG 259 1731 GGCAUCUCACUUUAUGAUA 97 1731 GGCAUCUCACUUUAUGAUA 97 1749 UAUCAUAAAGUGAGAUGCC 260 1749 AGGGAAGGCUACUACCUAG 98 1749 AGGGAAGGCUACUACCUAG 98 1767 CUAGGUAGUAGCCUUCCCU 261 1767 GGGCACUUUAAGUCAGUGA 99 1767 GGGCACUUUAAGUCAGUGA 99 1785 UCACUGACUUAAAGUGCCC 262 1785 ACAGCCCCUUAUUUGCACU 100 1785 ACAGCCCCUUAUUUGCACU 100 1803 AGUGCAAAUAAGGGGCUGU 263 1803 UUCACCUUUUGACCAUAAC 101 1803 UUCACCUUUUGACCAUAAC 101 1821 GUUAUGGUCAAAAGGUGAA 264 1821 CUGUUUCCCCAGAGCAGGA 102 1821 CUGUUUCCCCAGAGCAGGA 102 1839 UCCUGCUCUGGGGAAACAG 265 1839 AGCUUGUGGAAAUACCUUG 103 1839 AGCUUGUGGAAAUACCUUG 103 1857 CAAGGUAUUUCCACAAGCU 266 1857 GGCUGAUGUUGCAGCCUGC 104 1857 GGCUGAUGUUGCAGCCUGC 104 1875 GCAGGCUGCAACAUCAGCC 267 1875 CAGCAAGUGCUUCCGUCUC 105 1875 CAGCAAGUGCUUCCGUCUC 105 1893 GAGACGGAAGCACUUGCUG 268 1893 CCGGAAUCCUUGGGGAGCA 106 1893 CCGGAAUCCUUGGGGAGCA 106 1911 UGCUCCCCAAGGAUUCCGG 269 1911 ACUUGUCCACGUCUUUUCU 107 1911 ACUUGUCCACGUCUUUUCU 107 1929 AGAAAAGACGUGGACAAGU 270 1929 UCAUAUCAUGGUAGUCACU 108 1929 UCAUAUCAUGGUAGUCACU 108 1947 AGUGACUACCAUGAUAUGA 271 1947 UAACAUAUAUAAGGUAUGU 109 1947 UAACAUAUAUAAGGUAUGU 109 1965 ACAUACCUUAUAUAUGUUA 272 1965 UGCUAUUGGCCCAGCUUUU 110 1965 UGCUAUUGGCCCAGCUUUU 110 1983 AAAAGCUGGGCCAAUAGCA 273 1983 UAGAAAAUGCAGUCAUUUU 111 1983 UAGAAAAUGCAGUCAUUUU 111 2001 AAAAUGACUGCAUUUUCUA 274 2001 UUCUAAAUAAAAAGGAAGU 112 2001 UUCUAAAUAAAAAGGAAGU 112 2019 ACUUCCUUUUUAUUUAGAA 275 2019 UACUGCACCCAGCAGUGUC 113 2019 UACUGCACCCAGCAGUGUC 113 2037 GACACUGCUGGGUGCAGUA 276 2037 CACUCUGUAGUUACUGUGG 114 2037 CACUCUGUAGUUACUGUGG 114 2055 CCACAGUAACUACAGAGUG 277 2055 GUCACUUGUACCAUAUAGA 115 2055 GUCACUUGUACCAUAUAGA 115 2073 UCUAUAUGGUACAAGUGAC 278 2073 AGGUGUAACACUUGUCAAG 116 2073 AGGUGUAACACUUGUCAAG 116 2091 CUUGACAAGUGUUACACCU 279 2091 GAAGCGUUAUGUGCAGUAC 117 2091 GAAGCGUUAUGUGCAGUAC 117 2109 GUACUGCACAUAACGCUUC 280 2109 CUUAAUGUUUGUAAGACUU 118 2109 CUUAAUGUUUGUAAGACUU 118 2127 AAGUCUUACAAACAUUAAG 281 2127 UACAAAAAAAGAUUUAAAG 119 2127 UACAAAAAAAGAUUUAAAG 119 2145 CUUUAAAUCUUUUUUUGUA 282 2145 GUGGCAGCUUCACUCGACA 120 2145 GUGGCAGCUUCACUCGACA 120 2163 UGUCGAGUGAAGCUGCCAC 283 2163 AUUUGGUGAGAGAAGUACA 121 2163 AUUUGGUGAGAGAAGUACA 121 2181 UGUACUUCUCUCACCAAAU 284 2181 AAAGGUUGCAGUGCUGAGC 122 2181 AAAGGUUGCAGUGCUGAGC 122 2199 GCUCAGCACUGCAACCUUU 285 2199 CUGUGGGCGGUUUCUGGGG 123 2199 CUGUGGGCGGUUUCUGGGG 123 2217 CCCCAGAAACCGCCCACAG 286 2217 GAUGUCCCAGGGUGGAACU 124 2217 GAUGUCCCAGGGUGGAACU 124 2235 AGUUCCACCCUGGGACAUC 287 2235 UCCACAUGCUGGUGCAUAU 125 2235 UCCACAUGCUGGUGCAUAU 125 2253 AUAUGCACCAGCAUGUGGA 288 2253 UACGCCCUUGAGCUACUUC 126 2253 UACGCCCUUGAGCUACUUC 126 2271 GAAGUAGCUCAAGGGCGUA 289 2271 CAAAUGUGGUUUAUACCUC 127 2271 CAAAUGUGGUUUAUACCUC 127 2289 GAGGUAUAAACCACAUUUG 290 2289 CGCAGAUACAAGAAUCUUU 128 2289 CGCAGAUACAAGAAUCUUU 128 2307 AAAGAUUCUUGUAUCUGCG 291 2307 UAUGAAUAUACAAUUCUUU 129 2307 UAUGAAUAUACAAUUCUUU 129 2325 AAAGAAUUGUAUAUUCAUA 292 2325 UUUCCUUCUACAGCUUAGC 130 2325 UUUCCUUCUACAGCUUAGC 130 2343 GCUAAGCUGUAGAAGGAAA 293 2343 CUCCGUCUUUUCAACCACG 131 2343 CUCCGUCUUUUCAACCACG 131 2361 CGUGGUUGAAAAGACGGAG 294 2361 GAACAUUUAAAACCCGACC 132 2361 GAACAUUUAAAACCCGACC 132 2379 GGUCGGGUUUUAAAUGUUC 295 2379 CUACUAGCACUGUUCUGUC 133 2379 CUACUAGCACUGUUCUGUC 133 2397 GACAGAACAGUGCUAGUAG 296 2397 CCUCAAGUACUCAAAUAUU 134 2397 CCUCAAGUACUCAAAUAUU 134 2415 AAUAUUUGAGUACUUGAGG 297 2415 UUCUGAUACUGCUGAGUCA 135 2415 UUCUGAUACUGCUGAGUCA 135 2433 UGACUCAGCAGUAUCAGAA 298 2433 AGACUGUCAGAAAAAGCUA 136 2433 AGACUGUCAGAAAAAGCUA 136 2451 UAGCUUUUUCUGACAGUCU 299 2451 AGCACUAACUCGUGUUUGG 137 2451 AGCACUAACUCGUGUUUGG 137 2469 CCAAACACGAGUUAGUGCU 300 2469 GAGCUCUAUCCAUAUUUUA 138 2469 GAGCUCUAUCCAUAUUUUA 138 2487 UAAAAUAUGGAUAGAGCUC 301 2487 ACUGAUCUCUUUAAGUAUU 139 2487 ACUGAUCUCUUUAAGUAUU 139 2505 AAUACUUAAAGAGAUCAGU 302 2505 UUGUUCCUGCCACUGUGUA 140 2505 UUGUUCCUGCCACUGUGUA 140 2523 UACACAGUGGCAGGAACAA 303 2523 ACUGUGGAGUUGACUCGGU 141 2523 ACUGUGGAGUUGACUCGGU 141 2541 ACCGAGUCAACUCCACAGU 304 2541 UGUUCUGUCCCAGUGCGGU 142 2541 UGUUCUGUCCCAGUGCGGU 142 2559 ACCGCACUGGGACAGAACA 305 2559 UGCCUCCUCUUGACUUCCC 143 2559 UGCCUCCUCUUGACUUCCC 143 2577 GGGAAGUCAAGAGGAGGCA 306 2577 CCACUGCUCUCUGUGGUGA 144 2577 CCACUGCUCUCUGUGGUGA 144 2595 UCACCACAGAGAGCAGUGG 307 2595 AGAAAUUUGCCUUGUUCAA 145 2595 AGAAAUUUGCCUUGUUCAA 145 2613 UUGAACAAGGCAAAUUUCU 308 2613 AUAAUUACUGUACCCUCGC 146 2613 AUAAUUACUGUACCCUCGC 146 2631 GCGAGGGUACAGUAAUUAU 309 2631 CAUGACUGUUACAGCUUUC 147 2631 CAUGACUGUUACAGCUUUC 147 2649 GAAAGCUGUAACAGUCAUG 310 2649 CUGUGCAGAGAUGACUGUC 148 2649 CUGUGCAGAGAUGACUGUC 148 2667 GACAGUCAUCUCUGCACAG 311 2667 CCAAGUGCCACAUGCCUAC 149 2667 CCAAGUGCCACAUGCCUAC 149 2685 GUAGGCAUGUGGCACUUGG 312 2685 CGAUUGAAAUGAAAACUCU 150 2685 CGAUUGAAAUGAAAACUCU 150 2703 AGAGUUUUCAUUUCAAUCG 313 2703 UAUUGUUACCUCUGAGUUG 151 2703 UAUUGUUACCUCUGAGUUG 151 2721 CAACUCAGAGGUAACAAUA 314 2721 GUGUUCCACGGAAAAUGCU 152 2721 GUGUUCCACGGAAAAUGCU 152 2739 AGCAUUUUCCGUGGAACAC 315 2739 UAUCCAGCAGAUCAUUUAG 153 2739 UAUCCAGCAGAUCAUUUAG 153 2757 CUAAAUGAUCUGCUGGAUA 316 2757 GGAAAAAUAAUUCUAUUUU 154 2757 GGAAAAAUAAUUCUAUUUU 154 2775 AAAAUAGAAUUAUUUUUCC 317 2775 UUAGCUUUUCAUUUCUCAG 155 2775 UUAGCUUUUCAUUUCUCAG 155 2793 CUGAGAAAUGAAAAGCUAA 318 2793 GCUGUCCUUUUUUCUUGUU 156 2793 GCUGUCCUUUUUUCUUGUU 156 2811 AACAAGAAAAAAGGACAGC 319 2811 UUGAUUUUUGACAGCAAUG 157 2811 UUGAUUUUUGACAGCAAUG 157 2829 CAUUGCUGUCAAAAAUCAA 320 2829 GGAGAAUGGGUUAUAUAAA 158 2829 GGAGAAUGGGUUAUAUAAA 158 2847 UUUAUAUAACCCAUUCUCC 321 2847 AGACUGCCUGCUAAUAUGA 159 2847 AGACUGCCUGCUAAUAUGA 159 2865 UCAUAUUAGCAGGCAGUCU 322 2865 AACAGAAAUGCAUUUGUAA 160 2865 AACAGAAAUGCAUUUGUAA 160 2883 UUACAAAUGCAUUUCUGUU 323 2883 AUUCAUGAAAAUAAAUGUA 161 2883 AUUCAUGAAAAUAAAUGUA 161 2901 UACAUUUAUUUUCAUGAAU 324 2901 ACAUCUUCUAUCUUCAAAA 162 2901 ACAUCUUCUAUCUUCAAAA 162 2919 UUUUGAAGAUAGAAGAUGU 325 2913 UUCAAAAAAAAAAAAAAAA 163 2913 UUCAAAAAAAAAAAAAAAA 163 2931 UUUUUUUUUUUUUUUUGAA 326 Seq Seq Seq Pos Target Sequence ID UPos Upper seq ID LPos Lower seq ID XM_055766.6 (MAPK3/ERK1) 3 CGGGGCCUCGGGCGGGGCC 327 3 CGGGGCCUCGGGCGGGGCC 327 21 GGCCCCGCCCGAGGCCCCG 432 21 CGCCGUGGGGAGGAGGGCG 328 21 CGCCGUGGGGAGGAGGGCG 328 39 CGCCCUCCUCCCCACGGCG 433 39 GGUGGGAGGGGAGGAGUGG 329 39 GGUGGGAGGGGAGGAGUGG 329 57 CCACUCCUCCCCUCCCACC 434 57 GAGAUGGCGGCGGCGGCGG 330 57 GAGAUGGCGGCGGCGGCGG 330 75 CCGCCGCCGCCGCCAUCUC 435 75 GCUCAGGGGGGCGGGGGCG 331 75 GCUCAGGGGGGCGGGGGCG 331 93 CGCCCCCGCCCCCCUGAGC 436 93 GGGGAGCCCCGUAGAACCG 332 93 GGGGAGCCCCGUAGAACCG 332 111 CGGUUCUACGGGGCUCCCC 437 111 GAGGGGGUCGGCCCGGGGG 333 111 GAGGGGGUCGGCCCGGGGG 333 129 CCCCCGGGCCGACCCCCUC 438 129 GUCCCGGGGGAGGUGGAGA 334 129 GUCCCGGGGGAGGUGGAGA 334 147 UCUCCACCUCCCCCGGGAC 439 147 AUGGUGAAGGGGCAGCCGU 335 147 AUGGUGAAGGGGCAGCCGU 335 165 ACGGCUGCCCCUUCACCAU 440 165 UUCGACGUGGGCCCGCGCU 336 165 UUCGACGUGGGCCCGCGCU 336 183 AGCGCGGGCCCACGUCGAA 441 183 UACACGCAGUUGCAGUACA 337 183 UACACGCAGUUGCAGUACA 337 201 UGUACUGCAACUGCGUGUA 442 201 AUCGGCGAGGGCGCGUACG 338 201 AUCGGCGAGGGCGCGUACG 338 219 CGUACGCGCCCUCGCCGAU 443 219 GGCAUGGUCAGCUCGGCCU 339 219 GGCAUGGUCAGCUCGGCCU 339 237 AGGCCGAGCUGACCAUGCC 444 237 UAUGACCACGUGCGCAAGA 340 237 UAUGACCACGUGCGCAAGA 340 255 UCUUGCGCACGUGGUCAUA 445 255 ACUCGCGUGGCCAUCAAGA 341 255 ACUCGCGUGGCCAUCAAGA 341 273 UCUUGAUGGCCACGCGAGU 446 273 AAGAUCAGCCCCUUCGAAC 342 273 AAGAUCAGCCCCUUCGAAC 342 291 GUUCGAAGGGGCUGAUCUU 447 291 CAUCAGACCUACUGCCAGC 343 291 CAUCAGACCUACUGCCAGC 343 309 GCUGGCAGUAGGUCUGAUG 448 309 CGCACGCUCCGGGAGAUCC 344 309 CGCACGCUCCGGGAGAUCC 344 327 GGAUCUCCCGGAGCGUGCG 449 327 CAGAUCCUGCUGCGCUUCC 345 327 CAGAUCCUGCUGCGCUUCC 345 345 GGAAGCGCAGCAGGAUCUG 450 345 CGCCAUGAGAAUGUCAUCG 346 345 CGCCAUGAGAAUGUCAUCG 346 363 CGAUGACAUUCUCAUGGCG 451 363 GGCAUCCGAGACAUUCUGC 347 363 GGCAUCCGAGACAUUCUGC 347 381 GCAGAAUGUCUCGGAUGCC 452 381 CGGGCGUCCACCCUGGAAG 348 381 CGGGCGUCCACCCUGGAAG 348 399 CUUCCAGGGUGGACGCCCG 453 399 GCCAUGAGAGAUGUCUACA 349 399 GCCAUGAGAGAUGUCUACA 349 417 UGUAGACAUCUCUCAUGGC 454 417 AUUGUGCAGGACCUGAUGG 350 417 AUUGUGCAGGACCUGAUGG 350 435 CCAUCAGGUCCUGCACAAU 455 435 GAGACUGACCUGUACAAGU 351 435 GAGACUGACCUGUACAAGU 351 453 ACUUGUACAGGUCAGUCUC 456 453 UUGCUGAAAAGCCAGCAGC 352 453 UUGCUGAAAAGCCAGCAGC 352 471 GCUGCUGGCUUUUCAGCAA 457 471 CUGAGCAAUGACCAUAUCU 353 471 CUGAGCAAUGACCAUAUCU 353 489 AGAUAUGGUCAUUGCUCAG 458 489 UGCUACUUCCUCUACCAGA 354 489 UGCUACUUCCUCUACCAGA 354 507 UCUGGUAGAGGAAGUAGCA 459 507 AUCCUGCGGGGCCUCAAGU 355 507 AUCCUGCGGGGCCUCAAGU 355 525 ACUUGAGGCCCCGCAGGAU 460 525 UACAUCCACUCCGCCAACG 356 525 UACAUCCACUCCGCCAACG 356 543 CGUUGGCGGAGUGGAUGUA 461 543 GUGCUCCACCGAGAUCUAA 357 543 GUGCUCCACCGAGAUCUAA 357 561 UUAGAUCUCGGUGGAGCAC 462 561 AAGCCCUCCAACCUGCUCA 358 561 AAGCCCUCCAACCUGCUCA 358 579 UGAGCAGGUUGGAGGGCUU 463 579 AUCAACACCACCUGCGACC 359 579 AUCAACACCACCUGCGACC 359 597 GGUCGCAGGUGGUGUUGAU 464 597 CUUAAGAUUUGUGAUUUCG 360 597 CUUAAGAUUUGUGAUUUCG 360 615 CGAAAUCACAAAUCUUAAG 465 615 GGCCUGGCCCGGAUUGCCG 361 615 GGCCUGGCCCGGAUUGCCG 361 633 CGGCAAUCCGGGCCAGGCC 466 633 GAUCCUGAGCAUGACCACA 362 633 GAUCCUGAGCAUGACCACA 362 651 UGUGGUCAUGCUCAGGAUC 467 651 ACCGGCUUCCUGACGGAGU 363 651 ACCGGCUUCCUGACGGAGU 363 669 ACUCCGUCAGGAAGCCGGU 468 669 UAUGUGGCUACGCGCUGGU 364 669 UAUGUGGCUACGCGCUGGU 364 687 ACCAGCGCGUAGCCACAUA 469 687 UACCGGGCCCCAGAGAUCA 365 687 UACCGGGCCCCAGAGAUCA 365 705 UGAUCUCUGGGGCCCGGUA 470 705 AUGCUGAACUCCAAGGGCU 366 705 AUGCUGAACUCCAAGGGCU 366 723 AGCCCUUGGAGUUCAGCAU 471 723 UAUACCAAGUCCAUCGACA 367 723 UAUACCAAGUCCAUCGACA 367 741 UGUCGAUGGACUUGGUAUA 472 741 AUCUGGUCUGUGGGCUGCA 368 741 AUCUGGUCUGUGGGCUGCA 368 759 UGCAGCCCACAGACCAGAU 473 759 AUUCUGGCUGAGAUGCUCU 369 759 AUUCUGGCUGAGAUGCUCU 369 777 AGAGCAUCUCAGCCAGAAU 474 777 UCUAACCGGCCCAUCUUCC 370 777 UCUAACCGGCCCAUCUUCC 370 795 GGAAGAUGGGCCGGUUAGA 475 795 CCUGGCAAGCACUACCUGG 371 795 CCUGGCAAGCACUACCUGG 371 813 CCAGGUAGUGCUUGCCAGG 476 813 GAUCAGCUCAACCACAUUC 372 813 GAUCAGCUCAACCACAUUC 372 831 GAAUGUGGUUGAGCUGAUC 477 831 CUGGGCAUCCUGGGCUCCC 373 831 CUGGGCAUCCUGGGCUCCC 373 849 GGGAGCCCAGGAUGCCCAG 478 849 CCAUCCCAGGAGGACCUGA 374 849 CCAUCCCAGGAGGACCUGA 374 867 UCAGGUCCUCCUGGGAUGG 479 867 AAUUGUAUCAUCAACAUGA 375 867 AAUUGUAUCAUCAACAUGA 375 885 UCAUGUUGAUGAUACAAUU 480 885 AAGGCCCGAAACUACCUAC 376 885 AAGGCCCGAAACUACCUAC 376 903 GUAGGUAGUUUCGGGCCUU 481 903 CAGUCUCUGCCCUCCAAGA 377 903 CAGUCUCUGCCCUCCAAGA 377 921 UCUUGGAGGGCAGAGACUG 482 921 ACCAAGGUGGCUUGGGCCA 378 921 ACCAAGGUGGCUUGGGCCA 378 939 UGGCCCAAGCCACCUUGGU 483 939 AAGCUUUUCCCCAAGUCAG 379 939 AAGCUUUUCCCCAAGUCAG 379 957 CUGACUUGGGGAAAAGCUU 484 957 GACUCCAAAGCCCUUGACC 380 957 GACUCCAAAGCCCUUGACC 380 975 GGUCAAGGGCUUUGGAGUC 485 975 CUGCUGGACCGGAUGUUAA 381 975 CUGCUGGACCGGAUGUUAA 381 993 UUAACAUCCGGUCCAGCAG 486 993 ACCUUUAACCCCAAUAAAC 382 993 ACCUUUAACCCCAAUAAAC 382 1011 GUUUAUUGGGGUUAAAGGU 487 1011 CGGAUCACAGUGGAGGAAG 383 1011 CGGAUCACAGUGGAGGAAG 383 1029 CUUCCUCCACUGUGAUCCG 488 1029 GCGCUGGCUCACCCCUACC 384 1029 GCGCUGGCUCACCCCUACC 384 1047 GGUAGGGGUGAGCCAGCGC 489 1047 CUGGAGCAGUACUAUGACC 385 1047 CUGGAGCAGUACUAUGACC 385 1065 GGUCAUAGUACUGCUCCAG 490 1065 CCGACGGAUGAGCCAGUGG 386 1065 CCGACGGAUGAGCCAGUGG 386 1083 CCACUGGCUCAUCCGUCGG 491 1083 GCCGAGGAGCCCUUCACCU 387 1083 GCCGAGGAGCCCUUCACCU 387 1101 AGGUGAAGGGCUCCUCGGC 492 1101 UUCGCCAUGGAGCUGGAUG 388 1101 UUCGCCAUGGAGCUGGAUG 388 1119 CAUCCAGCUCCAUGGCGAA 493 1119 GACCUACCUAAGGAGCGGC 389 1119 GACCUACCUAAGGAGCGGC 389 1137 GCCGCUCCUUAGGUAGGUC 494 1137 CUGAAGGAGCUCAUCUUCC 390 1137 CUGAAGGAGCUCAUCUUCC 390 1155 GGAAGAUGAGCUCCUUCAG 495 1155 CAGGAGACAGCACGCUUCC 391 1155 CAGGAGACAGCACGCUUCC 391 1173 GGAAGCGUGCUGUCUCCUG 496 1173 CAGCCCGGAGUGCUGGAGG 392 1173 CAGCCCGGAGUGCUGGAGG 392 1191 CCUCCAGCACUCCGGGCUG 497 1191 GCCCCCUAGCCCAGACAGA 393 1191 GCCCCCUAGCCCAGACAGA 393 1209 UCUGUCUGGGCUAGGGGGC 498 1209 ACAUCUCUGCACCCUGGGG 394 1209 ACAUCUCUGCACCCUGGGG 394 1227 CCCCAGGGUGCAGAGAUGU 499 1227 GCCUGGAACAGAACUGGCA 395 1227 GCCUGGAACAGAACUGGCA 395 1245 UGCCAGUUCUGUUCCAGGC 500 1245 AAAGAGGCAAGAGGUCACU 396 1245 AAAGAGGCAAGAGGUCACU 396 1263 AGUGACCUCUUGCCUCUUU 501 1263 UGAGGGCCUCUGUCACCCA 397 1263 UGAGGGCCUCUGUCACCCA 397 1281 UGGGUGACAGAGGCCCUCA 502 1281 AGGACCUGCCUCCUGCCUG 398 1281 AGGACCUGCCUCCUGCCUG 398 1299 CAGGCAGGAGGCAGGUCCU 503 1299 GCCCCUCUCCCGCCAGACU 399 1299 GCCCCUCUCCCGCCAGACU 399 1317 AGUCUGGCGGGAGAGGGGC 504 1317 UGUUAGAAAAUGGACACUG 400 1317 UGUUAGAAAAUGGACACUG 400 1335 CAGUGUCCAUUUUCUAACA 505 1335 GUGCCCAGCCCGGACCUUG 401 1335 GUGCCCAGCCCGGACCUUG 401 1353 CAAGGUCCGGGCUGGGCAC 506 1353 GGCAGCCCAGGCCGGGGUG 402 1353 GGCAGCCCAGGCCGGGGUG 402 1371 CACCCCGGCCUGGGCUGCC 507 1371 GGAGCAUGGGCCUGGCCAC 403 1371 GGAGCAUGGGCCUGGCCAC 403 1389 GUGGCCAGGCCCAUGCUCC 508 1389 CCUCUCUCCUUUGCUGAGG 404 1389 CCUCUCUCCUUUGCUGAGG 404 1407 CCUCAGCAAAGGAGAGAGG 509 1407 GCCUCCAGCUUCAGGCAGG 405 1407 GCCUCCAGCUUCAGGCAGG 405 1425 CCUGCCUGAAGCUGGAGGC 510 1425 GCCAAGGCCUUCUCCUCCC 406 1425 GCCAAGGCCUUCUCCUCCC 406 1443 GGGAGGAGAAGGCCUUGGC 511 1443 CCACCCGCCCUCCCCACGG 407 1443 CCACCCGCCCUCCCCACGG 407 1461 CCGUGGGGAGGGCGGGUGG 512 1461 GGGCCUCGGGACCUCAGGU 408 1461 GGGCCUCGGGACCUCAGGU 408 1479 ACCUGAGGUCCCGAGGCCC 513 1479 UGGCCCCAGUUCAAUCUCC 409 1479 UGGCCCCAGUUCAAUCUCC 409 1497 GGAGAUUGAACUGGGGCCA 514 1497 CCGCUGCUGCUGCUGCGCC 410 1497 CCGCUGCUGCUGCUGCGCC 410 1515 GGCGCAGCAGCAGCAGCGG 515 1515 CCUUACCUUCCCCAGCGUC 411 1515 CCUUACCUUCCCCAGCGUC 411 1533 GACGCUGGGGAAGGUAAGG 516 1533 CCCAGUCUCUGGCAGUUCU 412 1533 CCCAGUCUCUGGCAGUUCU 412 1551 AGAACUGCCAGAGACUGGG 517 1551 UGGAAUGGAAGGGUUCUGG 413 1551 UGGAAUGGAAGGGUUCUGG 413 1569 CCAGAACCCUUCCAUUCCA 518 1569 GCUGCCCCAACCUGCUGAA 414 1569 GCUGCCCCAACCUGCUGAA 414 1587 UUCAGCAGGUUGGGGCAGC 519 1587 AGGGCAGAGGUGGAGGGUG 415 1587 AGGGCAGAGGUGGAGGGUG 415 1605 CACCCUCCACCUCUGCCCU 520 1605 GGGGGGCGCUGAGUAGGGA 416 1605 GGGGGGCGCUGAGUAGGGA 416 1623 UCCCUACUCAGCGCCCCCC 521 1623 ACUCAGGGCCAUGCCUGCC 417 1623 ACUCAGGGCCAUGCCUGCC 417 1641 GGCAGGCAUGGCCCUGAGU 522 1641 CCCCCUCAUCUCAUUCAAA 418 1641 CCCCCUCAUCUCAUUCAAA 418 1659 UUUGAAUGAGAUGAGGGGG 523 1659 ACCCCACCCUAGUUUCCCU 419 1659 ACCCCACCCUAGUUUCCCU 419 1677 AGGGAAACUAGGGUGGGGU 524 1677 UGAAGGAACAUUCCUUAGU 420 1677 UGAAGGAACAUUCCUUAGU 420 1695 ACUAAGGAAUGUUCCUUCA 525 1695 UCUCAAGGGCUAGCAUCCC 421 1695 UCUCAAGGGCUAGCAUCCC 421 1713 GGGAUGCUAGCCCUUGAGA 526 1713 CUGAGGAGCCAGGCCGGGC 422 1713 CUGAGGAGCCAGGCCGGGC 422 1731 GCCCGGCCUGGCUCCUCAG 527 1731 CCGAAUCCCCUCCCUGUCA 423 1731 CCGAAUCCCCUCCCUGUCA 423 1749 UGACAGGGAGGGGAUUCGG 528 1749 AAAGCUGUCACUUCGCGUG 424 1749 AAAGCUGUCACUUCGCGUG 424 1767 CACGCGAAGUGACAGCUUU 529 1767 GCCCUCGCUGCUUCUGUGU 425 1767 GCCCUCGCUGCUUCUGUGU 425 1785 ACACAGAAGCAGCGAGGGC 530 1785 UGUGGUGAGCAGAAGUGGA 426 1785 UGUGGUGAGCAGAAGUGGA 426 1803 UCCACUUCUGCUCACCACA 531 1803 AGCUGGGGGGCGUGGAGAG 427 1803 AGCUGGGGGGCGUGGAGAG 427 1821 CUCUCCACGCCCCCCAGCU 532 1821 GCCCGGCGCCCCUGCCACC 428 1821 GCCCGGCGCCCCUGCCACC 428 1839 GGUGGCAGGGGCGCCGGGC 533 1839 CUCCCUGACCCGUCUAAUA 429 1839 CUCCCUGACCCGUCUAAUA 429 1857 UAUUAGACGGGUCAGGGAG 534 1857 AUAUAAAUAUAGAGAUGUG 430 1857 AUAUAAAUAUAGAGAUGUG 430 1875 CACAUCUCUAUAUUUAUAU 535 1865 AUAGAGAUGUGUCUAUGGC 431 1865 AUAGAGAUGUGUCUAUGGC 431 1883 GCCAUAGACACAUCUCUAU 536 ID Seq Seq Pos Target Sequence Seq UPos Upper seq ID LPos Lower seq ID NM_002750 (MAPK8/JNK1) 3 UAAUUGCUUGCCAUCAUGA 537 3 UAAUUGCUUGCCAUCAUGA 537 21 UCAUGAUGGCAAGCAAUUA 616 21 AGCAGAAGCAAGCGUGACA 538 21 AGCAGAAGCAAGCGUGACA 538 39 UGUCACGCUUGCUUCUGCU 617 39 AACAAUUUUUAUAGUGUAG 539 39 AACAAUUUUUAUAGUGUAG 539 57 CUACACUAUAAAAAUUGUU 618 57 GAGAUUGGAGAUUCUACAU 540 57 GAGAUUGGAGAUUCUACAU 540 75 AUGUAGAAUCUCCAAUCUC 619 75 UUCACAGUCCUGAAACGAU 541 75 UUCACAGUCCUGAAACGAU 541 93 AUCGUUUCAGGACUGUGAA 620 93 UAUCAGAAUUUAAAACCUA 542 93 UAUCAGAAUUUAAAACCUA 542 111 UAGGUUUUAAAUUCUGAUA 621 111 AUAGGCUCAGGAGCUCAAG 543 111 AUAGGCUCAGGAGCUCAAG 543 129 CUUGAGCUCCUGAGCCUAU 622 129 GGAAUAGUAUGCGCAGCUU 544 129 GGAAUAGUAUGCGCAGCUU 544 147 AAGCUGCGCAUACUAUUCC 623 147 UAUGAUGCCAUUCUUGAAA 545 147 UAUGAUGCCAUUCUUGAAA 545 165 UUUCAAGAAUGGCAUCAUA 624 165 AGAAAUGUUGCAAUCAAGA 546 165 AGAAAUGUUGCAAUCAAGA 546 183 UCUUGAUUGCAACAUUUCU 625 183 AAGCUAAGCCGACCAUUUC 547 183 AAGCUAAGCCGACCAUUUC 547 201 GAAAUGGUCGGCUUAGCUU 626 201 CAGAAUCAGACUCAUGCCA 548 201 CAGAAUCAGACUCAUGCCA 548 219 UGGCAUGAGUCUGAUUCUG 627 219 AAGCGGGCCUACAGAGAGC 549 219 AAGCGGGCCUACAGAGAGC 549 237 GCUCUCUGUAGGCCCGCUU 628 237 CUAGUUCUUAUGAAAUGUG 550 237 CUAGUUCUUAUGAAAUGUG 550 255 CACAUUUCAUAAGAACUAG 629 255 GUUAAUCACAAAAAUAUAA 551 255 GUUAAUCACAAAAAUAUAA 551 273 UUAUAUUUUUGUGAUUAAC 630 273 AUUGGCCUUUUGAAUGUUU 552 273 AUUGGCCUUUUGAAUGUUU 552 291 AAACAUUCAAAAGGCCAAU 631 291 UUCACACCACAGAAAUCCC 553 291 UUCACACCACAGAAAUCCC 553 309 GGGAUUUCUGUGGUGUGAA 632 309 CUAGAAGAAUUUCAAGAUG 554 309 CUAGAAGAAUUUCAAGAUG 554 327 CAUCUUGAAAUUCUUCUAG 633 327 GUUUACAUAGUCAUGGAGC 555 327 GUUUACAUAGUCAUGGAGC 555 345 GCUCCAUGACUAUGUAAAC 634 345 CUCAUGGAUGCAAAUCUUU 556 345 CUCAUGGAUGCAAAUCUUU 556 363 AAAGAUUUGCAUCCAUGAG 635 363 UGCCAAGUGAUUCAGAUGG 557 363 UGCCAAGUGAUUCAGAUGG 557 381 CCAUCUGAAUCACUUGGCA 636 381 GAGCUAGAUCAUGAAAGAA 558 381 GAGCUAGAUCAUGAAAGAA 558 399 UUCUUUCAUGAUCUAGCUC 637 399 AUGUCCUACCUUCUCUAUC 559 399 AUGUCCUACCUUCUCUAUC 559 417 GAUAGAGAAGGUAGGACAU 638 417 CAGAUGCUGUGUGGAAUCA 560 417 CAGAUGCUGUGUGGAAUCA 560 435 UGAUUCCACACAGCAUCUG 639 435 AAGCACCUUCAUUCUGCUG 561 435 AAGCACCUUCAUUCUGCUG 561 453 CAGCAGAAUGAAGGUGCUU 640 453 GGAAUUAUUCAUCGGGACU 562 453 GGAAUUAUUCAUCGGGACU 562 471 AGUCCCGAUGAAUAAUUCC 641 471 UUAAAGCCCAGUAAUAUAG 563 471 UUAAAGCCCAGUAAUAUAG 563 489 CUAUAUUACUGGGCUUUAA 642 489 GUAGUAAAAUCUGAUUGCA 564 489 GUAGUAAAAUCUGAUUGCA 564 507 UGCAAUCAGAUUUUACUAC 643 507 ACUUUGAAGAUUCUUGACU 565 507 ACUUUGAAGAUUCUUGACU 565 525 AGUCAAGAAUCUUCAAAGU 644 525 UUCGGUCUGGCCAGGACUG 566 525 UUCGGUCUGGCCAGGACUG 566 543 CAGUCCUGGCCAGACCGAA 645 543 GCAGGAACGAGUUUUAUGA 567 543 GCAGGAACGAGUUUUAUGA 567 561 UCAUAAAACUCGUUCCUGC 646 561 AUGACGCCUUAUGUAGUGA 568 561 AUGACGCCUUAUGUAGUGA 568 579 UCACUACAUAAGGCGUCAU 647 579 ACUCGCUACUACAGAGCAC 569 579 ACUCGCUACUACAGAGCAC 569 597 GUGCUCUGUAGUAGCGAGU 648 597 CCCGAGGUCAUCCUUGGCA 570 597 CCCGAGGUCAUCCUUGGCA 570 615 UGCCAAGGAUGACCUCGGG 649 615 AUGGGCUACAAGGAAAACG 571 615 AUGGGCUACAAGGAAAACG 571 633 CGUUUUCCUUGUAGCCCAU 650 633 GUGGAUUUAUGGUCUGUGG 572 633 GUGGAUUUAUGGUCUGUGG 572 651 CCACAGACCAUAAAUCCAC 651 651 GGGUGCAUUAUGGGAGAAA 573 651 GGGUGCAUUAUGGGAGAAA 573 669 UUUCUCCCAUAAUGCACCC 652 669 AUGGUUUGCCACAAAAUCC 574 669 AUGGUUUGCCACAAAAUCC 574 687 GGAUUUUGUGGCAAACCAU 653 687 CUCUUUCCAGGAAGGGACU 575 687 CUCUUUCCAGGAAGGGACU 575 705 AGUCCCUUCCUGGAAAGAG 654 705 UAUAUUGAUCAGUGGAAUA 576 705 UAUAUUGAUCAGUGGAAUA 576 723 UAUUCCACUGAUCAAUAUA 655 723 AAAGUUAUUGAACAGCUUG 577 723 AAAGUUAUUGAACAGCUUG 577 741 CAAGCUGUUCAAUAACUUU 656 741 GGAACACCAUGUCCUGAAU 578 741 GGAACACCAUGUCCUGAAU 578 759 AUUCAGGACAUGGUGUUCC 657 759 UUCAUGAAGAAACUGCAAC 579 759 UUCAUGAAGAAACUGCAAC 579 777 GUUGCAGUUUCUUCAUGAA 658 777 CCAACAGUAAGGACUUACG 580 777 CCAACAGUAAGGACUUACG 580 795 CGUAAGUCCUUACUGUUGG 659 795 GUUGAAAACAGACCUAAAU 581 795 GUUGAAAACAGACCUAAAU 581 813 AUUUAGGUCUGUUUUCAAC 660 813 UAUGCUGGAUAUAGCUUUG 582 813 UAUGCUGGAUAUAGCUUUG 582 831 CAAAGCUAUAUCCAGCAUA 661 831 GAGAAACUCUUCCCUGAUG 583 831 GAGAAACUCUUCCCUGAUG 583 849 CAUCAGGGAAGAGUUUCUC 662 849 GUCCUUUUCCCAGCUGACU 584 849 GUCCUUUUCCCAGCUGACU 584 867 AGUCAGCUGGGAAAAGGAC 663 867 UCAGAACACAACAAACUUA 585 867 UCAGAACACAACAAACUUA 585 885 UAAGUUUGUUGUGUUCUGA 664 885 AAAGCCAGUCAGGCAAGGG 586 885 AAAGCCAGUCAGGCAAGGG 586 903 CCCUUGCCUGACUGGCUUU 665 903 GAUUUGUUAUCCAAAAUGC 587 903 GAUUUGUUAUCCAAAAUGC 587 921 GCAUUUUGGAUAACAAAUC 666 921 CUGGUAAUAGAUGCAUCUA 588 921 CUGGUAAUAGAUGCAUCUA 588 939 UAGAUGCAUCUAUUACCAG 667 939 AAAAGGAUCUCUGUAGAUG 589 939 AAAAGGAUCUCUGUAGAUG 589 957 CAUCUACAGAGAUCCUUUU 668 957 GAAGCUCUCCAACACCCGU 590 957 GAAGCUCUCCAACACCCGU 590 975 ACGGGUGUUGGAGAGCUUC 669 975 UACAUCAAUGUCUGGUAUG 591 975 UACAUCAAUGUCUGGUAUG 591 993 CAUACCAGACAUUGAUGUA 670 993 GAUCCUUCUGAAGCAGAAG 592 993 GAUCCUUCUGAAGCAGAAG 592 1011 CUUCUGCUUCAGAAGGAUC 671 1011 GCUCCACCACCAAAGAUCC 593 1011 GCUCCACCACCAAAGAUCC 593 1029 GGAUCUUUGGUGGUGGAGC 672 1029 CCUGACAAGCAGUUAGAUG 594 1029 CCUGACAAGCAGUUAGAUG 594 1047 CAUCUAACUGCUUGUCAGG 673 1047 GAAAGGGAACACACAAUAG 595 1047 GAAAGGGAACACACAAUAG 595 1065 CUAUUGUGUGUUCCCUUUC 674 1065 GAAGAGUGGAAAGAAUUGA 596 1065 GAAGAGUGGAAAGAAUUGA 596 1083 UCAAUUCUUUCCACUCUUC 675 1083 AUAUAUAAGGAAGUUAUGG 597 1083 AUAUAUAAGGAAGUUAUGG 597 1101 CCAUAACUUCCUUAUAUAU 676 1101 GACUUGGAGGAGAGAACCA 598 1101 GACUUGGAGGAGAGAACCA 598 1119 UGGUUCUCUCCUCCAAGUC 677 1119 AAGAAUGGAGUUAUACGGG 599 1119 AAGAAUGGAGUUAUACGGG 599 1137 CCCGUAUAACUCCAUUCUU 678 1137 GGGCAGCCCUCUCCUUUAG 600 1137 GGGCAGCCCUCUCCUUUAG 600 1155 CUAAAGGAGAGGGCUGCCC 679 1155 GCACAGGUGCAGCAGUGAU 601 1155 GCACAGGUGCAGCAGUGAU 601 1173 AUCACUGCUGCACCUGUGC 680 1173 UCAAUGGCUCUCAGCAUCC 602 1173 UCAAUGGCUCUCAGCAUCC 602 1191 GGAUGCUGAGAGCCAUUGA 681 1191 CAUCAUCAUCGUCGUCUGU 603 1191 CAUCAUCAUCGUCGUCUGU 603 1209 ACAGACGACGAUGAUGAUG 682 1209 UCAAUGAUGUGUCUUCAAU 604 1209 UCAAUGAUGUGUCUUCAAU 604 1227 AUUGAAGACACAUCAUUGA 683 1227 UGUCAACAGAUCCGACUUU 605 1227 UGUCAACAGAUCCGACUUU 605 1245 AAAGUCGGAUCUGUUGACA 684 1245 UGGCCUCUGAUACAGACAG 606 1245 UGGCCUCUGAUACAGACAG 606 1263 CUGUCUGUAUCAGAGGCCA 685 1263 GCAGUCUAGAAGCAGCAGC 607 1263 GCAGUCUAGAAGCAGCAGC 607 1281 GCUGCUGCUUCUAGACUGC 686 1281 CUGGGCCUCUGGGCUGCUG 608 1281 CUGGGCCUCUGGGCUGCUG 608 1299 CAGCAGCCCAGAGGCCCAG 687 1299 GUAGAUGACUACUUGGGCC 609 1299 GUAGAUGACUACUUGGGCC 609 1317 GGCCCAAGUAGUCAUCUAC 688 1317 CAUCGGGGGGUGGGAGGGA 610 1317 CAUCGGGGGGUGGGAGGGA 610 1335 UCCCUCCCACCCCCCGAUG 689 1335 AUGGGGAGUCGGUUAGUCA 611 1335 AUGGGGAGUCGGUUAGUCA 611 1353 UGACUAACCGACUCCCCAU 690 1353 AUUGAUAGAACUACUUUGA 612 1353 AUUGAUAGAACUACUUUGA 612 1371 UCAAAGUAGUUCUAUCAAU 691 1371 AAAACAAUUCAGUGGUCUU 613 1371 AAAACAAUUCAGUGGUCUU 613 1389 AAGACCACUGAAUUGUUUU 692 1389 UAUUUUUGGGUGAUUUUUC 614 1389 UAUUUUUGGGUGAUUUUUC 614 1407 GAAAAAUCACCCAAAAAUA 693 1397 GGUGAUUUUUCAAAAAAUG 615 1397 GGUGAUUUUUCAAAAAAUG 615 1415 CAUUUUUUGAAAAAUCACC 694 ID Seq Seq Pos Target Sequence Seq UPos Upper seq ID LPos Lower seq ID NM_139012 (MAPK14/p38) 3 AACCGCGACCACUGGAGCC 695 3 AACCGCGACCACUGGAGCC 695 21 GGCUCCAGUGGUCGCGGUU 904 21 CUUAGCGGGCGCAGCAGCU 696 21 CUUAGCGGGCGCAGCAGCU 696 39 AGCUGCUGCGCCCGCUAAG 905 39 UGGAACGGGAGUACUGCGA 697 39 UGGAACGGGAGUACUGCGA 697 57 UCGCAGUACUCCCGUUCCA 906 57 ACGCAGCCCGGAGUCGGCC 698 57 ACGCAGCCCGGAGUCGGCC 698 75 GGCCGACUCCGGGCUGCGU 907 75 CUUGUAGGGGCGAAGGUGC 699 75 CUUGUAGGGGCGAAGGUGC 699 93 GCACCUUCGCCCCUACAAG 908 93 CAGGGAGAUCGCGGCGGGC 700 93 CAGGGAGAUCGCGGCGGGC 700 111 GCCCGCCGCGAUCUCCCUG 909 111 CGCAGUCUUGAGCGCCGGA 701 111 CGCAGUCUUGAGCGCCGGA 701 129 UCCGGCGCUCAAGACUGCG 910 129 AGCGCGUCCCUGCCCUUAG 702 129 AGCGCGUCCCUGCCCUUAG 702 147 CUAAGGGCAGGGACGCGCU 911 147 GCGGGGCUUGCCCCAGUCG 703 147 GCGGGGCUUGCCCCAGUCG 703 165 CGACUGGGGCAAGCCCCGC 912 165 GCAGGGGCACAUCCAGCCG 704 165 GCAGGGGCACAUCCAGCCG 704 183 CGGCUGGAUGUGCCCCUGC 913 183 GCUGCGGCUGACAGCAGCC 705 183 GCUGCGGCUGACAGCAGCC 705 201 GGCUGCUGUCAGCCGCAGC 914 201 CGCGCGCGCGGGAGUCUGC 706 201 CGCGCGCGCGGGAGUCUGC 706 219 GCAGACUCCCGCGCGCGCG 915 219 CGGGGUCGCGGCAGCCGCA 707 219 CGGGGUCGCGGCAGCCGCA 707 237 UGCGGCUGCCGCGACCCCG 916 237 ACCUGCGCGGGCGACCAGC 708 237 ACCUGCGCGGGCGACCAGC 708 255 GCUGGUCGCCCGCGCAGGU 917 255 CGCAAGGUCCCCGCCCGGC 709 255 CGCAAGGUCCCCGCCCGGC 709 273 GCCGGGCGGGGACCUUGCG 918 273 CUGGGCGGGCAGCAAGGGC 710 273 CUGGGCGGGCAGCAAGGGC 710 291 GCCCUUGCUGCCCGCCCAG 919 291 CCGGGGAGAGGGUGCGGGU 711 291 CCGGGGAGAGGGUGCGGGU 711 309 ACCCGCACCCUCUCCCCGG 920 309 UGCAGGCGGGGGCCCCACA 712 309 UGCAGGCGGGGGCCCCACA 712 327 UGUGGGGCCCCCGCCUGCA 921 327 AGGGCCACCUUCUUGCCCG 713 327 AGGGCCACCUUCUUGCCCG 713 345 CGGGCAAGAAGGUGGCCCU 922 345 GGCGGCUGCCGCUGGAAAA 714 345 GGCGGCUGCCGCUGGAAAA 714 363 UUUUCCAGCGGCAGCCGCC 923 363 AUGUCUCAGGAGAGGCCCA 715 363 AUGUCUCAGGAGAGGCCCA 715 381 UGGGCCUCUCCUGAGACAU 924 381 ACGUUCUACCGGCAGGAGC 716 381 ACGUUCUACCGGCAGGAGC 716 399 GCUCCUGCCGGUAGAACGU 925 399 CUGAACAAGACAAUCUGGG 717 399 CUGAACAAGACAAUCUGGG 717 417 CCCAGAUUGUCUUGUUCAG 926 417 GAGGUGCCCGAGCGUUACC 718 417 GAGGUGCCCGAGCGUUACC 718 435 GGUAACGCUCGGGCACCUC 927 435 CAGAACCUGUCUCCAGUGG 719 435 CAGAACCUGUCUCCAGUGG 719 453 CCACUGGAGACAGGUUCUG 928 453 GGCUCUGGCGCCUAUGGCU 720 453 GGCUCUGGCGCCUAUGGCU 720 471 AGCCAUAGGCGCCAGAGCC 929 471 UCUGUGUGUGCUGCUUUUG 721 471 UCUGUGUGUGCUGCUUUUG 721 489 CAAAAGCAGCACACACAGA 930 489 GACACAAAAACGGGGUUAC 722 489 GACACAAAAACGGGGUUAC 722 507 GUAACCCCGUUUUUGUGUC 931 507 CGUGUGGCAGUGAAGAAGC 723 507 CGUGUGGCAGUGAAGAAGC 723 525 GCUUCUUCACUGCCACACG 932 525 CUCUCCAGACCAUUUCAGU 724 525 CUCUCCAGACCAUUUCAGU 724 543 ACUGAAAUGGUCUGGAGAG 933 543 UCCAUCAUUCAUGCGAAAA 725 543 UCCAUCAUUCAUGCGAAAA 725 561 UUUUCGCAUGAAUGAUGGA 934 561 AGAACCUACAGAGAACUGC 726 561 AGAACCUACAGAGAACUGC 726 579 GCAGUUCUCUGUAGGUUCU 935 579 CGGUUACUUAAACAUAUGA 727 579 CGGUUACUUAAACAUAUGA 727 597 UCAUAUGUUUAAGUAACCG 936 597 AAACAUGAAAAUGUGAUUG 728 597 AAACAUGAAAAUGUGAUUG 728 615 CAAUCACAUUUUCAUGUUU 937 615 GGUCUGUUGGACGUUUUUA 729 615 GGUCUGUUGGACGUUUUUA 729 633 UAAAAACGUCCAACAGACC 938 633 ACACCUGCAAGGUCUCUGG 730 633 ACACCUGCAAGGUCUCUGG 730 651 CCAGAGACCUUGCAGGUGU 939 651 GAGGAAUUCAAUGAUGUGU 731 651 GAGGAAUUCAAUGAUGUGU 731 669 ACACAUCAUUGAAUUCCUC 940 669 UAUCUGGUGACCCAUCUCA 732 669 UAUCUGGUGACCCAUCUCA 732 687 UGAGAUGGGUCACCAGAUA 941 687 AUGGGGGCAGAUCUGAACA 733 687 AUGGGGGCAGAUCUGAACA 733 705 UGUUCAGAUCUGCCCCCAU 942 705 AACAUUGUGAAAUGUCAGA 734 705 AACAUUGUGAAAUGUCAGA 734 723 UCUGACAUUUCACAAUGUU 943 723 AAGCUUACAGAUGACCAUG 735 723 AAGCUUACAGAUGACCAUG 735 741 CAUGGUCAUCUGUAAGCUU 944 741 GUUCAGUUCCUUAUCUACC 736 741 GUUCAGUUCCUUAUCUACC 736 759 GGUAGAUAAGGAACUGAAC 945 759 CAAAUUCUCCGAGGUCUAA 737 759 CAAAUUCUCCGAGGUCUAA 737 777 UUAGACCUCGGAGAAUUUG 946 777 AAGUAUAUACAUUCAGCUG 738 777 AAGUAUAUACAUUCAGCUG 738 795 CAGCUGAAUGUAUAUACUU 947 795 GACAUAAUUCACAGGGACC 739 795 GACAUAAUUCACAGGGACC 739 813 GGUCCCUGUGAAUUAUGUC 948 813 CUAAAACCUAGUAAUCUAG 740 813 CUAAAACCUAGUAAUCUAG 740 831 CUAGAUUACUAGGUUUUAG 949 831 GCUGUGAAUGAAGACUGUG 741 831 GCUGUGAAUGAAGACUGUG 741 849 CACAGUCUUCAUUCACAGC 950 849 GAGCUGAAGAUUCUGGAUU 742 849 GAGCUGAAGAUUCUGGAUU 742 867 AAUCCAGAAUCUUCAGCUC 951 867 UUUGGACUGGCUCGGCACA 743 867 UUUGGACUGGCUCGGCACA 743 885 UGUGCCGAGCCAGUCCAAA 952 885 ACAGAUGAUGAAAUGACAG 744 885 ACAGAUGAUGAAAUGACAG 744 903 CUGUCAUUUCAUCAUCUGU 953 903 GGCUACGUGGCCACUAGGU 745 903 GGCUACGUGGCCACUAGGU 745 921 ACCUAGUGGCCACGUAGCC 954 921 UGGUACAGGGCUCCUGAGA 746 921 UGGUACAGGGCUCCUGAGA 746 939 UCUCAGGAGCCCUGUACCA 955 939 AUCAUGCUGAACUGGAUGC 747 939 AUCAUGCUGAACUGGAUGC 747 957 GCAUCCAGUUCAGCAUGAU 956 957 CAUUACAACCAGACAGUUG 748 957 CAUUACAACCAGACAGUUG 748 975 CAACUGUCUGGUUGUAAUG 957 975 GAUAUUUGGUCAGUGGGAU 749 975 GAUAUUUGGUCAGUGGGAU 749 993 AUCCCACUGACCAAAUAUC 958 993 UGCAUAAUGGCCGAGCUGU 750 993 UGCAUAAUGGCCGAGCUGU 750 1011 ACAGCUCGGCCAUUAUGCA 959 1011 UUGACUGGAAGAACAUUGU 751 1011 UUGACUGGAAGAACAUUGU 751 1029 ACAAUGUUCUUCCAGUCAA 960 1029 UUUCCUGGUACAGACCAUA 752 1029 UUUCCUGGUACAGACCAUA 752 1047 UAUGGUCUGUACCAGGAAA 961 1047 AUUGAUCAGUUGAAGCUCA 753 1047 AUUGAUCAGUUGAAGCUCA 753 1065 UGAGCUUCAACUGAUCAAU 962 1065 AUUUUAAGACUCGUUGGAA 754 1065 AUUUUAAGACUCGUUGGAA 754 1083 UUCCAACGAGUCUUAAAAU 963 1083 ACCCCAGGGGCUGAGCUUU 755 1083 ACCCCAGGGGCUGAGCUUU 755 1101 AAAGCUCAGCCCCUGGGGU 964 1101 UUGAAGAAAAUCUCCUCAG 756 1101 UUGAAGAAAAUCUCCUCAG 756 1119 CUGAGGAGAUUUUCUUCAA 965 1119 GAGUCUGCAAGAAACUAUA 757 1119 GAGUCUGCAAGAAACUAUA 757 1137 UAUAGUUUCUUGCAGACUC 966 1137 AUUCAGUCUUUGACUCAGA 758 1137 AUUCAGUCUUUGACUCAGA 758 1155 UCUGAGUCAAAGACUGAAU 967 1155 AUGCCGAAGAUGAACUUUG 759 1155 AUGCCGAAGAUGAACUUUG 759 1173 CAAAGUUCAUCUUCGGCAU 968 1173 GCGAAUGUAUUUAUUGGUG 760 1173 GCGAAUGUAUUUAUUGGUG 760 1191 CACCAAUAAAUACAUUCGC 969 1191 GCCAAUCCCCUGGCUGUCG 761 1191 GCCAAUCCCCUGGCUGUCG 761 1209 CGACAGCCAGGGGAUUGGC 970 1209 GACUUGCUGGAGAAGAUGC 762 1209 GACUUGCUGGAGAAGAUGC 762 1227 GCAUCUUCUCCAGCAAGUC 971 1227 CUUGUAUUGGACUCAGAUA 763 1227 CUUGUAUUGGACUCAGAUA 763 1245 UAUCUGAGUCCAAUACAAG 972 1245 AAGAGAAUUACAGCGGCCC 764 1245 AAGAGAAUUACAGCGGCCC 764 1263 GGGCCGCUGUAAUUCUCUU 973 1263 CAAGCCCUUGCACAUGCCU 765 1263 CAAGCCCUUGCACAUGCCU 765 1281 AGGCAUGUGCAAGGGCUUG 974 1281 UACUUUGCUCAGUACCACG 766 1281 UACUUUGCUCAGUACCACG 766 1299 CGUGGUACUGAGCAAAGUA 975 1299 GAUCCUGAUGAUGAACCAG 767 1299 GAUCCUGAUGAUGAACCAG 767 1317 CUGGUUCAUCAUCAGGAUC 976 1317 GUGGCCGAUCCUUAUGAUC 768 1317 GUGGCCGAUCCUUAUGAUC 768 1335 GAUCAUAAGGAUCGGCCAC 977 1335 CAGUCCUUUGAAAGCAGGG 769 1335 CAGUCCUUUGAAAGCAGGG 769 1353 CCCUGCUUUCAAAGGACUG 978 1353 GACCUCCUUAUAGAUGAGU 770 1353 GACCUCCUUAUAGAUGAGU 770 1371 ACUCAUCUAUAAGGAGGUC 979 1371 UGGAAAAGCCUGACCUAUG 771 1371 UGGAAAAGCCUGACCUAUG 771 1389 CAUAGGUCAGGCUUUUCCA 980 1389 GAUGAAGUCAUCAGCUUUG 772 1389 GAUGAAGUCAUCAGCUUUG 772 1407 CAAAGCUGAUGACUUCAUC 981 1407 GUGCCACCACCCCUUGACC 773 1407 GUGCCACCACCCCUUGACC 773 1425 GGUCAAGGGGUGGUGGCAC 982 1425 CAAGAAGAGAUGGAGUCCU 774 1425 CAAGAAGAGAUGGAGUCCU 774 1443 AGGACUCCAUCUCUUCUUG 983 1443 UGAGCACCUGGUUUCUGUU 775 1443 UGAGCACCUGGUUUCUGUU 775 1461 AACAGAAACCAGGUGCUCA 984 1461 UCUGUUGAUCCCACUUCAC 776 1461 UCUGUUGAUCCCACUUCAC 776 1479 GUGAAGUGGGAUCAACAGA 985 1479 CUGUGAGGGGAAGGCCUUU 777 1479 CUGUGAGGGGAAGGCCUUU 777 1497 AAAGGCCUUCCCCUCACAG 986 1497 UUCACGGGAACUCUCCAAA 778 1497 UUCACGGGAACUCUCCAAA 778 1515 UUUGGAGAGUUCCCGUGAA 987 1515 AUAUUAUUCAAGUGCCUCU 779 1515 AUAUUAUUCAAGUGCCUCU 779 1533 AGAGGCACUUGAAUAAUAU 988 1533 UUGUUGCAGAGAUUUCCUC 780 1533 UUGUUGCAGAGAUUUCCUC 780 1551 GAGGAAAUCUCUGCAACAA 989 1551 CCAUGGUGGAAGGGGGUGU 781 1551 CCAUGGUGGAAGGGGGUGU 781 1569 ACACCCCCUUCCACCAUGG 990 1569 UGCGUGCGUGUGCGUGCGU 782 1569 UGCGUGCGUGUGCGUGCGU 782 1587 ACGCACGCACACGCACGCA 991 1587 UGUUAGUGUGUGUGCAUGU 783 1587 UGUUAGUGUGUGUGCAUGU 783 1605 ACAUGCACACACACUAACA 992 1605 UGUGUGUCUGUCUUUGUGG 784 1605 UGUGUGUCUGUCUUUGUGG 784 1623 CCACAAAGACAGACACACA 993 1623 GGAGGGUAAGACAAUAUGA 785 1623 GGAGGGUAAGACAAUAUGA 785 1641 UCAUAUUGUCUUACCCUCC 994 1641 AACAAACUAUGAUCACAGU 786 1641 AACAAACUAUGAUCACAGU 786 1659 ACUGUGAUCAUAGUUUGUU 995 1659 UGACUUUACAGGAGGUUGU 787 1659 UGACUUUACAGGAGGUUGU 787 1677 ACAACCUCCUGUAAAGUCA 996 1677 UGGAUGCUCCAGGGCAGCC 788 1677 UGGAUGCUCCAGGGCAGCC 788 1695 GGCUGCCCUGGAGCAUCCA 997 1695 CUCCACCUUGCUCUUCUUU 789 1695 CUCCACCUUGCUCUUCUUU 789 1713 AAAGAAGAGCAAGGUGGAG 998 1713 UCUGAGAGUUGGCUCAGGC 790 1713 UCUGAGAGUUGGCUCAGGC 790 1731 GCCUGAGCCAACUCUCAGA 999 1731 CAGACAAGAGCUGCUGUCC 791 1731 CAGACAAGAGCUGCUGUCC 791 1749 GGACAGCAGCUCUUGUCUG 1000 1749 CUUUUAGGAAUAUGUUCAA 792 1749 CUUUUAGGAAUAUGUUCAA 792 1767 UUGAACAUAUUCCUAAAAG 1001 1767 AUGCAAAGUAAAAAAAUAU 793 1767 AUGCAAAGUAAAAAAAUAU 793 1785 AUAUUUUUUUACUUUGCAU 1002 1785 UGAAUUGUCCCCAAUCCCG 794 1785 UGAAUUGUCCCCAAUCCCG 794 1803 CGGGAUUGGGGACAAUUCA 1003 1803 GGUCAUGCUUUUGCCACUU 795 1803 GGUCAUGCUUUUGCCACUU 795 1821 AAGUGGCAAAAGCAUGACC 1004 1821 UUGGCUUCUCCUGUGACCC 796 1821 UUGGCUUCUCCUGUGACCC 796 1839 GGGUCACAGGAGAAGCCAA 1005 1839 CCACCUUGACGGUGGGGCG 797 1839 CCACCUUGACGGUGGGGCG 797 1857 CGCCCCACCGUCAAGGUGG 1006 1857 GUAGACUUGACAACAUCCC 798 1857 GUAGACUUGACAACAUCCC 798 1875 GGGAUGUUGUCAAGUCUAC 1007 1875 CACAGUGGCACGGAGAGAA 799 1875 CACAGUGGCACGGAGAGAA 799 1893 UUCUCUCCGUGCCACUGUG 1008 1893 AGGCCCAUACCUUCUGGUU 800 1893 AGGCCCAUACCUUCUGGUU 800 1911 AACCAGAAGGUAUGGGCCU 1009 1911 UGCUUCAGACCUGACACCG 801 1911 UGCUUCAGACCUGACACCG 801 1929 CGGUGUCAGGUCUGAAGCA 1010 1929 GUCCCUCAGUGAUACGUAC 802 1929 GUCCCUCAGUGAUACGUAC 802 1947 GUACGUAUCACUGAGGGAC 1011 1947 CAGCCAAAAAGGACCAACU 803 1947 CAGCCAAAAAGGACCAACU 803 1965 AGUUGGUCCUUUUUGGCUG 1012 1965 UGGCUUCUGUGCACUAGCC 804 1965 UGGCUUCUGUGCACUAGCC 804 1983 GGCUAGUGCACAGAAGCCA 1013 1983 CUGUGAUUAACUUGCUUAG 805 1983 CUGUGAUUAACUUGCUUAG 805 2001 CUAAGCAAGUUAAUCACAG 1014 2001 GUAUGGUUCUCAGAUCUUG 806 2001 GUAUGGUUCUCAGAUCUUG 806 2019 CAAGAUCUGAGAACCAUAC 1015 2019 GACAGUAUAUUUGAAACUG 807 2019 GACAGUAUAUUUGAAACUG 807 2037 CAGUUUCAAAUAUACUGUC 1016 2037 GUAAAUAUGUUUGUGCCUU 808 2037 GUAAAUAUGUUUGUGCCUU 808 2055 AAGGCACAAACAUAUUUAC 1017 2055 UAAAAGGAGAGAAGAAAGU 809 2055 UAAAAGGAGAGAAGAAAGU 809 2073 ACUUUCUUCUCUCCUUUUA 1018 2073 UGUAGAUAGUUAAAAGACU 810 2073 UGUAGAUAGUUAAAAGACU 810 2091 AGUCUUUUAACUAUCUACA 1019 2091 UGCAGCUGCUGAAGUUCUG 811 2091 UGCAGCUGCUGAAGUUCUG 811 2109 CAGAACUUCAGCAGCUGCA 1020 2109 GAGCCGGGCAAGUCGAGAG 812 2109 GAGCCGGGCAAGUCGAGAG 812 2127 CUCUCGACUUGCCCGGCUC 1021 2127 GGGCUGUUGGACAGCUGCU 813 2127 GGGCUGUUGGACAGCUGCU 813 2145 AGCAGCUGUCCAACAGCCC 1022 2145 UUGUGGGCCCGGAGUAAUC 814 2145 UUGUGGGCCCGGAGUAAUC 814 2163 GAUUACUCCGGGCCCACAA 1023 2163 CAGGCAGCCUUCAUAGGCG 815 2163 CAGGCAGCCUUCAUAGGCG 815 2181 CGCCUAUGAAGGCUGCCUG 1024 2181 GGUCAUGUGUGCAUGUGAG 816 2181 GGUCAUGUGUGCAUGUGAG 816 2199 CUCACAUGCACACAUGACC 1025 2199 GCACAUGCGUAUAUGUGCG 817 2199 GCACAUGCGUAUAUGUGCG 817 2217 CGCACAUAUACGCAUGUGC 1026 2217 GUCUCUCUUUCUCCCUCAC 818 2217 GUCUCUCUUUCUCCCUCAC 818 2235 GUGAGGGAGAAAGAGAGAC 1027 2235 CCCCCAGGUGUUGCCAUUU 819 2235 CCCCCAGGUGUUGCCAUUU 819 2253 AAAUGGCAACACCUGGGGG 1028 2253 UCUCUGCUUACCCUUCACC 820 2253 UCUCUGCUUACCCUUCACC 820 2271 GGUGAAGGGUAAGCAGAGA 1029 2271 CUUUGGUGCAGAGGUUUCU 821 2271 CUUUGGUGCAGAGGUUUCU 821 2289 AGAAACCUCUGCACCAAAG 1030 2289 UUGAAUAUCUGCCCCAGUA 822 2289 UUGAAUAUCUGCCCCAGUA 822 2307 UACUGGGGCAGAUAUUCAA 1031 2307 AGUCAGAAGCAGGUUCUUG 823 2307 AGUCAGAAGCAGGUUCUUG 823 2325 CAAGAACCUGCUUCUGACU 1032 2325 GAUGUCAUGUACUUCCUGU 824 2325 GAUGUCAUGUACUUCCUGU 824 2343 ACAGGAAGUACAUGACAUC 1033 2343 UGUACUCUUUAUUUCUAGC 825 2343 UGUACUCUUUAUUUCUAGC 825 2361 GCUAGAAAUAAAGAGUACA 1034 2361 CAGAGUGAGGAUGUGUUUU 826 2361 CAGAGUGAGGAUGUGUUUU 826 2379 AAAACACAUCCUCACUCUG 1035 2379 UGCACGUCUUGCUAUUUGA 827 2379 UGCACGUCUUGCUAUUUGA 827 2397 UCAAAUAGCAAGACGUGCA 1036 2397 AGCAUGCACAGCUGCUUGU 828 2397 AGCAUGCACAGCUGCUUGU 828 2415 ACAAGCAGCUGUGCAUGCU 1037 2415 UCCUGCUCUCUUCAGGAGG 829 2415 UCCUGCUCUCUUCAGGAGG 829 2433 CCUCCUGAAGAGAGCAGGA 1038 2433 GCCCUGGUGUCAGGCAGGU 830 2433 GCCCUGGUGUCAGGCAGGU 830 2451 ACCUGCCUGACACCAGGGC 1039 2451 UUUGCCAGUGAAGACUUCU 831 2451 UUUGCCAGUGAAGACUUCU 831 2469 AGAAGUCUUCACUGGCAAA 1040 2469 UUGGGUAGUUUAGAUCCCA 832 2469 UUGGGUAGUUUAGAUCCCA 832 2487 UGGGAUCUAAACUACCCAA 1041 2487 AUGUCACCUCAGCUGAUAU 833 2487 AUGUCACCUCAGCUGAUAU 833 2505 AUAUCAGCUGAGGUGACAU 1042 2505 UUAUGGCAAGUGAUAUCAC 834 2505 UUAUGGCAAGUGAUAUCAC 834 2523 GUGAUAUCACUUGCCAUAA 1043 2523 CCUCUCUUCAGCCCCUAGU 835 2523 CCUCUCUUCAGCCCCUAGU 835 2541 ACUAGGGGCUGAAGAGAGG 1044 2541 UGCUAUUCUGUGUUGAACA 836 2541 UGCUAUUCUGUGUUGAACA 836 2559 UGUUCAACACAGAAUAGCA 1045 2559 ACAAUUGAUACUUCAGGUG 837 2559 ACAAUUGAUACUUCAGGUG 837 2577 CACCUGAAGUAUCAAUUGU 1046 2577 GCUUUUGAUGUGAAAAUCA 838 2577 GCUUUUGAUGUGAAAAUCA 838 2595 UGAUUUUCACAUCAAAAGC 1047 2595 AUGAAAAGAGGAACAGGUG 839 2595 AUGAAAAGAGGAACAGGUG 839 2613 CACCUGUUCCUCUUUUCAU 1048 2613 GGAUGUAUAGCAUUUUUAU 840 2613 GGAUGUAUAGCAUUUUUAU 840 2631 AUAAAAAUGCUAUACAUCC 1049 2631 UUCAUGCCAUCUGUUUUCA 841 2631 UUCAUGCCAUCUGUUUUCA 841 2649 UGAAAACAGAUGGCAUGAA 1050 2649 AACCAACUAUUUUUGAGGA 842 2649 AACCAACUAUUUUUGAGGA 842 2667 UCCUCAAAAAUAGUUGGUU 1051 2667 AAUUAUCAUGGGAAAAGAC 843 2667 AAUUAUCAUGGGAAAAGAC 843 2685 GUCUUUUCCCAUGAUAAUU 1052 2685 CCAGGGCUUUUCCCAGGAA 844 2685 CCAGGGCUUUUCCCAGGAA 844 2703 UUCCUGGGAAAAGCCCUGG 1053 2703 AUAUCCCAAACUUCGGAAA 845 2703 AUAUCCCAAACUUCGGAAA 845 2721 UUUCCGAAGUUUGGGAUAU 1054 2721 ACAAGUUAUUCUCUUCACU 846 2721 ACAAGUUAUUCUCUUCACU 846 2739 AGUGAAGAGAAUAACUUGU 1055 2739 UCCCAAUAACUAAUGCUAA 847 2739 UCCCAAUAACUAAUGCUAA 847 2757 UUAGCAUUAGUUAUUGGGA 1056 2757 AGAAAUGCUGAAAAUCAAA 848 2757 AGAAAUGCUGAAAAUCAAA 848 2775 UUUGAUUUUCAGCAUUUCU 1057 2775 AGUAAAAAAUUAAAGCCCA 849 2775 AGUAAAAAAUUAAAGCCCA 849 2793 UGGGCUUUAAUUUUUUACU 1058 2793 AUAAGGCCAGAAACUCCUU 850 2793 AUAAGGCCAGAAACUCCUU 850 2811 AAGGAGUUUCUGGCCUUAU 1059 2811 UUUGCUGUCUUUCUCUAAA 851 2811 UUUGCUGUCUUUCUCUAAA 851 2829 UUUAGAGAAAGACAGCAAA 1060 2829 AUAUGAUUACUUUAAAAUA 852 2829 AUAUGAUUACUUUAAAAUA 852 2847 UAUUUUAAAGUAAUCAUAU 1061 2847 AAAAAAGUAACAAGGUGUC 853 2847 AAAAAAGUAACAAGGUGUC 853 2865 GACACCUUGUUACUUUUUU 1062 2865 CUUUUCCACUCCUAUGGAA 854 2865 CUUUUCCACUCCUAUGGAA 854 2883 UUCCAUAGGAGUGGAAAAG 1063 2883 AAAGGGUCUUCUUGGCAGC 855 2883 AAAGGGUCUUCUUGGCAGC 855 2901 GCUGCCAAGAAGACCCUUU 1064 2901 CUUAACAUUGACUUCUUGG 856 2901 CUUAACAUUGACUUCUUGG 856 2919 CCAAGAAGUCAAUGUUAAG 1065 2919 GUUUGGGGAGAAAUAAAUU 857 2919 GUUUGGGGAGAAAUAAAUU 857 2937 AAUUUAUUUCUCCCCAAAC 1066 2937 UUUGUUUCAGAAUUUUGUA 858 2937 UUUGUUUCAGAAUUUUGUA 858 2955 UACAAAAUUCUGAAACAAA 1067 2955 AUAUUGUAGGAAUCCCUUU 859 2955 AUAUUGUAGGAAUCCCUUU 859 2973 AAAGGGAUUCCUACAAUAU 1068 2973 UGAGAAUGUGAUUCCUUUU 860 2973 UGAGAAUGUGAUUCCUUUU 860 2991 AAAAGGAAUCACAUUCUCA 1069 2991 UGAUGGGGAGAAAGGGCAA 861 2991 UGAUGGGGAGAAAGGGCAA 861 3009 UUGCCCUUUCUCCCCAUCA 1070 3009 AAUUAUUUUAAUAUUUUGU 862 3009 AAUUAUUUUAAUAUUUUGU 862 3027 ACAAAAUAUUAAAAUAAUU 1071 3027 UAUUUUCAACUUUAUAAAG 863 3027 UAUUUUCAACUUUAUAAAG 863 3045 CUUUAUAAAGUUGAAAAUA 1072 3045 GAUAAAAUAUCCUCAGGGG 864 3045 GAUAAAAUAUCCUCAGGGG 864 3063 CCCCUGAGGAUAUUUUAUC 1073 3063 GUGGAGAAGUGUCGUUUUC 865 3063 GUGGAGAAGUGUCGUUUUC 865 3081 GAAAACGACACUUCUCCAC 1074 3081 CAUAACUUGCUGAAUUUCA 866 3081 CAUAACUUGCUGAAUUUCA 866 3099 UGAAAUUCAGCAAGUUAUG 1075 3099 AGGCAUUUUGUUCUACAUG 867 3099 AGGCAUUUUGUUCUACAUG 867 3117 CAUGUAGAACAAAAUGCCU 1076 3117 GAGGACUCAUAUAUUUAAG 868 3117 GAGGACUCAUAUAUUUAAG 868 3135 CUUAAAUAUAUGAGUCCUC 1077 3135 GCCUUUUGUGUAAUAAGAA 869 3135 GCCUUUUGUGUAAUAAGAA 869 3153 UUCUUAUUACACAAAAGGC 1078 3153 AAGUAUAAAGUCACUUCCA 870 3153 AAGUAUAAAGUCACUUCCA 870 3171 UGGAAGUGACUUUAUACUU 1079 3171 AGUGUUGGCUGUGUGACAG 871 3171 AGUGUUGGCUGUGUGACAG 871 3189 CUGUCACACAGCCAACACU 1080 3189 GAAUCUUGUAUUUGGGCCA 872 3189 GAAUCUUGUAUUUGGGCCA 872 3207 UGGCCCAAAUACAAGAUUC 1081 3207 AAGGUGUUUCCAUUUCUCA 873 3207 AAGGUGUUUCCAUUUCUCA 873 3225 UGAGAAAUGGAAACACCUU 1082 3225 AAUCAGUGCAGUGAUACAU 874 3225 AAUCAGUGCAGUGAUACAU 874 3243 AUGUAUCACUGCACUGAUU 1083 3243 UGUACUCCAGAGGGACAGG 875 3243 UGUACUCCAGAGGGACAGG 875 3261 CCUGUCCCUCUGGAGUACA 1084 3261 GGUGGACCCCCUGAGUCAA 876 3261 GGUGGACCCCCUGAGUCAA 876 3279 UUGACUCAGGGGGUCCACC 1085 3279 ACUGGAGCAAGAAGGAAGG 877 3279 ACUGGAGCAAGAAGGAAGG 877 3297 CCUUCCUUCUUGCUCCAGU 1086 3297 GAGGCAGACUGAUGGCGAU 878 3297 GAGGCAGACUGAUGGCGAU 878 3315 AUCGCCAUCAGUCUGCCUC 1087 3315 UUCCCUCUCACCCGGGACU 879 3315 UUCCCUCUCACCCGGGACU 879 3333 AGUCCCGGGUGAGAGGGAA 1088 3333 UCUCCCCCUUUCAAGGAAA 880 3333 UCUCCCCCUUUCAAGGAAA 880 3351 UUUCCUUGAAAGGGGGAGA 1089 3351 AGUGAACCUUUAAAGUAAA 881 3351 AGUGAACCUUUAAAGUAAA 881 3369 UUUACUUUAAAGGUUCACU 1090 3369 AGGCCUCAUCUCCUUUAUU 882 3369 AGGCCUCAUCUCCUUUAUU 882 3387 AAUAAAGGAGAUGAGGCCU 1091 3387 UGCAGUUCAAAUCCUCACC 883 3387 UGCAGUUCAAAUCCUCACC 883 3405 GGUGAGGAUUUGAACUGCA 1092 3405 CAUCCACAGCAAGAUGAAU 884 3405 CAUCCACAGCAAGAUGAAU 884 3423 AUUCAUCUUGCUGUGGAUG 1093 3423 UUUUAUCAGCCAUGUUUGG 885 3423 UUUUAUCAGCCAUGUUUGG 885 3441 CCAAACAUGGCUGAUAAAA 1094 3441 GUUGUAAAUGCUCGUGUGA 886 3441 GUUGUAAAUGCUCGUGUGA 886 3459 UCACACGAGCAUUUACAAC 1095 3459 AUUUCCUACAGAAAUACUG 887 3459 AUUUCCUACAGAAAUACUG 887 3477 CAGUAUUUCUGUAGGAAAU 1096 3477 GCUCUGAAUAUUUUGUAAU 888 3477 GCUCUGAAUAUUUUGUAAU 888 3495 AUUACAAAAUAUUCAGAGC 1097 3495 UAAAGGUCUUUGCACAUGU 889 3495 UAAAGGUCUUUGCACAUGU 889 3513 ACAUGUGCAAAGACCUUUA 1098 3513 UGACCACAUACGUGUUAGG 890 3513 UGACCACAUACGUGUUAGG 890 3531 CCUAACACGUAUGUGGUCA 1099 3531 GAGGCUGCAUGCUCUGGAA 891 3531 GAGGCUGCAUGCUCUGGAA 891 3549 UUCCAGAGCAUGCAGCCUC 1100 3549 AGCCUGGACUCUAAGCUGG 892 3549 AGCCUGGACUCUAAGCUGG 892 3567 CCAGCUUAGAGUCCAGGCU 1101 3567 GAGCUCUUGGAAGAGCUCU 893 3567 GAGCUCUUGGAAGAGCUCU 893 3585 AGAGCUCUUCCAAGAGCUC 1102 3585 UUCGGUUUCUGAGCAUAAU 894 3585 UUCGGUUUCUGAGCAUAAU 894 3603 AUUAUGCUCAGAAACCGAA 1103 3603 UGCUCCCAUCUCCUGAUUU 895 3603 UGCUCCCAUCUCCUGAUUU 895 3621 AAAUCAGGAGAUGGGAGCA 1104 3621 UCUCUGAACAGAAAACAAA 896 3621 UCUCUGAACAGAAAACAAA 896 3639 UUUGUUUUCUGUUCAGAGA 1105 3639 AAGAGAGAAUGAGGGAAAU 897 3639 AAGAGAGAAUGAGGGAAAU 897 3657 AUUUCCCUCAUUCUCUCUU 1106 3657 UUGCUAUUUUAUUUGUAUU 898 3657 UUGCUAUUUUAUUUGUAUU 898 3675 AAUACAAAUAAAAUAGCAA 1107 3675 UCAUGAACUUGGCUGUAAU 899 3675 UCAUGAACUUGGCUGUAAU 899 3693 AUUACAGCCAAGUUCAUGA 1108 3693 UCAGUUAUGCCGUAUAGGA 900 3693 UCAGUUAUGCCGUAUAGGA 900 3711 UCCUAUACGGCAUAACUGA 1109 3711 AUGUCAGACAAUACCACUG 901 3711 AUGUCAGACAAUACCACUG 901 3729 CAGUGGUAUUGUCUGACAU 1110 3729 GGUUAAAAUAAAGCCUAUU 902 3729 GGUUAAAAUAAAGCCUAUU 902 3747 AAUAGGCUUUAUUUUAACC 1111 3737 UAAAGCCUAUUUUUCAAAU 903 3737 UAAAGCCUAUUUUUCAAAU 903 3755 AUUUGAAAAAUAGGCUUUA 1112 Seq Seq Seq Pos Seq ID UPos Upper seq ID LPos Lower seq ID hJUN NM_002228 3 AGUUGCACUGAGUGUGGCU 1247 3 AGUUGCACUGAGUGUGGCU 1247 21 AGCCACACUCAGUGCAACU 1428 21 UGAAGCAGCGAGGCGGGAG 1248 21 UGAAGCAGCGAGGCGGGAG 1248 39 CUCCCGCCUCGCUGCUUCA 1429 39 GUGGAGGUGCGCGGAGUCA 1249 39 GUGGAGGUGCGCGGAGUCA 1249 57 UGACUCCGCGCACCUCCAC 1430 57 AGGCAGACAGACAGACACA 1250 57 AGGCAGACAGACAGACACA 1250 75 UGUGUCUGUCUGUCUGCCU 1431 75 AGCCAGCCAGCCAGGUCGG 1251 75 AGCCAGCCAGCCAGGUCGG 1251 93 CCGACCUGGCUGGCUGGCU 1432 93 GCAGUAUAGUCCGAACUGC 1252 93 GCAGUAUAGUCCGAACUGC 1252 111 GCAGUUCGGACUAUACUGC 1433 111 CAAAUCUUAUUUUCUUUUC 1253 111 CAAAUCUUAUUUUCUUUUC 1253 129 GAAAAGAAAAUAAGAUUUG 1434 129 CACCUUCUCUCUAACUGCC 1254 129 CACCUUCUCUCUAACUGCC 1254 147 GGCAGUUAGAGAGAAGGUG 1435 147 CCAGAGCUAGCGCCUGUGG 1255 147 CCAGAGCUAGCGCCUGUGG 1255 165 CCACAGGCGCUAGCUCUGG 1436 165 GCUCCCGGGCUGGUGGUUC 1256 165 GCUCCCGGGCUGGUGGUUC 1256 183 GAACCACCAGCCCGGGAGC 1437 183 CGGGAGUGUCCAGAGAGCC 1257 183 CGGGAGUGUCCAGAGAGCC 1257 201 GGCUCUCUGGACACUCCCG 1438 201 CUUGUCUCCAGCCGGCCCC 1258 201 CUUGUCUCCAGCCGGCCCC 1258 219 GGGGCCGGCUGGAGACAAG 1439 219 CGGGAGGAGAGCCCUGCUG 1259 219 CGGGAGGAGAGCCCUGCUG 1259 237 CAGCAGGGCUCUCCUCCCG 1440 237 GCCCAGGCGCUGUUGACAG 1260 237 GCCCAGGCGCUGUUGACAG 1260 255 CUGUCAACAGCGCCUGGGC 1441 255 GCGGCGGAAAGCAGCGGUA 1261 255 GCGGCGGAAAGCAGCGGUA 1261 273 UACCGCUGCUUUCCGCCGC 1442 273 ACCCCACGCGCCCGCCGGG 1262 273 ACCCCACGCGCCCGCCGGG 1262 291 CCCGGCGGGCGCGUGGGGU 1443 291 GGGACGUCGGCGAGCGGCU 1263 291 GGGACGUCGGCGAGCGGCU 1263 309 AGCCGCUCGCCGACGUCCC 1444 309 UGCAGCAGCAAAGAACUUU 1264 309 UGCAGCAGCAAAGAACUUU 1264 327 AAAGUUCUUUGCUGCUGCA 1445 327 UCCCGGCGGGGAGGACCGG 1265 327 UCCCGGCGGGGAGGACCGG 1265 345 CCGGUCCUCCCCGCCGGGA 1446 345 GAGACAAGUGGCAGAGUCC 1266 345 GAGACAAGUGGCAGAGUCC 1266 363 GGACUCUGCCACUUGUCUC 1447 363 CCGGAGCGAACUUUUGCAA 1267 363 CCGGAGCGAACUUUUGCAA 1267 381 UUGCAAAAGUUCGCUCCGG 1448 381 AGCCUUUCCUGCGUCUUAG 1268 381 AGCCUUUCCUGCGUCUUAG 1268 399 CUAAGACGCAGGAAAGGCU 1449 399 GGCUUCUCCACGGCGGUAA 1269 399 GGCUUCUCCACGGCGGUAA 1269 417 UUACCGCCGUGGAGAAGCC 1450 417 AAGACCAGAAGGCGGCGGA 1270 417 AAGACCAGAAGGCGGCGGA 1270 435 UCCGCCGCCUUCUGGUCUU 1451 435 AGAGCCACGCAAGAGAAGA 1271 435 AGAGCCACGCAAGAGAAGA 1271 453 UCUUCUCUUGCGUGGCUCU 1452 453 AAGGACGUGCGCUCAGCUU 1272 453 AAGGACGUGCGCUCAGCUU 1272 471 AAGCUGAGCGCACGUCCUU 1453 471 UCGCUCGCACCGGUUGUUG 1273 471 UCGCUCGCACCGGUUGUUG 1273 489 CAACAACCGGUGCGAGCGA 1454 489 GAACUUGGGCGAGCGCGAG 1274 489 GAACUUGGGCGAGCGCGAG 1274 507 CUCGCGCUCGCCCAAGUUC 1455 507 GCCGCGGCUGCCGGGCGCC 1275 507 GCCGCGGCUGCCGGGCGCC 1275 525 GGCGCCCGGCAGCCGCGGC 1456 525 CCCCUCCCCCUAGCAGCGG 1276 525 CCCCUCCCCCUAGCAGCGG 1276 543 CCGCUGCUAGGGGGAGGGG 1457 543 GAGGAGGGGACAAGUCGUC 1277 543 GAGGAGGGGACAAGUCGUC 1277 561 GACGACUUGUCCCCUCCUC 1458 561 CGGAGUCCGGGCGGCCAAG 1278 561 CGGAGUCCGGGCGGCCAAG 1278 579 CUUGGCCGCCCGGACUCCG 1459 579 GACCCGCCGCCGGCCGGCC 1279 579 GACCCGCCGCCGGCCGGCC 1279 597 GGCCGGCCGGCGGCGGGUC 1460 597 CACUGCAGGGUCCGCACUG 1280 597 CACUGCAGGGUCCGCACUG 1280 615 CAGUGCGGACCCUGCAGUG 1461 615 GAUCCGCUCCGCGGGGAGA 1281 615 GAUCCGCUCCGCGGGGAGA 1281 633 UCUCCCCGCGGAGCGGAUC 1462 633 AGCCGCUGCUCUGGGAAGU 1282 633 AGCCGCUGCUCUGGGAAGU 1282 651 ACUUCCCAGAGCAGCGGCU 1463 651 UGAGUUCGCCUGCGGACUC 1283 651 UGAGUUCGCCUGCGGACUC 1283 669 GAGUCCGCAGGCGAACUCA 1464 669 CCGAGGAACCGCUGCGCCC 1284 669 CCGAGGAACCGCUGCGCCC 1284 687 GGGCGCAGCGGUUCCUCGG 1465 687 CGAAGAGCGCUCAGUGAGU 1285 687 CGAAGAGCGCUCAGUGAGU 1285 705 ACUCACUGAGCGCUCUUCG 1466 705 UGACCGCGACUUUUCAAAG 1286 705 UGACCGCGACUUUUCAAAG 1286 723 CUUUGAAAAGUCGCGGUCA 1467 723 GCCGGGUAGCGCGCGCGAG 1287 723 GCCGGGUAGCGCGCGCGAG 1287 741 CUCGCGCGCGCUACCCGGC 1468 741 GUCGACAAGUAAGAGUGCG 1288 741 GUCGACAAGUAAGAGUGCG 1288 759 CGCACUCUUACUUGUCGAC 1469 759 GGGAGGCAUCUUAAUUAAC 1289 759 GGGAGGCAUCUUAAUUAAC 1289 777 GUUAAUUAAGAUGCCUCCC 1470 777 CCCUGCGCUCCCUGGAGCG 1290 777 CCCUGCGCUCCCUGGAGCG 1290 795 CGCUCCAGGGAGCGCAGGG 1471 795 GAGCUGGUGAGGAGGGCGC 1291 795 GAGCUGGUGAGGAGGGCGC 1291 813 GCGCCCUCCUCACCAGCUC 1472 813 CAGCGGGGACGACAGCCAG 1292 813 CAGCGGGGACGACAGCCAG 1292 831 CUGGCUGUCGUCCCCGCUG 1473 831 GCGGGUGCGUGCGCUCUUA 1293 831 GCGGGUGCGUGCGCUCUUA 1293 849 UAAGAGCGCACGCACCCGC 1474 849 AGAGAAACUUUCCCUGUCA 1294 849 AGAGAAACUUUCCCUGUCA 1294 867 UGACAGGGAAAGUUUCUCU 1475 867 AAAGGCUCCGGGGGGCGCG 1295 867 AAAGGCUCCGGGGGGCGCG 1295 885 CGCGCCCCCCGGAGCCUUU 1476 885 GGGUGUCCCCCGCUUGCCA 1296 885 GGGUGUCCCCCGCUUGCCA 1296 903 UGGCAAGCGGGGGACACCC 1477 903 AGAGCCCUGUUGCGGCCCC 1297 903 AGAGCCCUGUUGCGGCCCC 1297 921 GGGGCCGCAACAGGGCUCU 1478 921 CGAAACUUGUGCGCGCACG 1298 921 CGAAACUUGUGCGCGCACG 1298 939 CGUGCGCGCACAAGUUUCG 1479 939 GCCAAACUAACCUCACGUG 1299 939 GCCAAACUAACCUCACGUG 1299 957 CACGUGAGGUUAGUUUGGC 1480 957 GAAGUGACGGACUGUUCUA 1300 957 GAAGUGACGGACUGUUCUA 1300 975 UAGAACAGUCCGUCACUUC 1481 975 AUGACUGCAAAGAUGGAAA 1301 975 AUGACUGCAAAGAUGGAAA 1301 993 UUUCCAUCUUUGCAGUCAU 1482 993 ACGACCUUCUAUGACGAUG 1302 993 ACGACCUUCUAUGACGAUG 1302 1011 CAUCGUCAUAGAAGGUCGU 1483 1011 GCCCUCAACGCCUCGUUCC 1303 1011 GCCCUCAACGCCUCGUUCC 1303 1029 GGAACGAGGCGUUGAGGGC 1484 1029 CUCCCGUCCGAGAGCGGAC 1304 1029 CUCCCGUCCGAGAGCGGAC 1304 1047 GUCCGCUCUCGGACGGGAG 1485 1047 CCUUAUGGCUACAGUAACC 1305 1047 CCUUAUGGCUACAGUAACC 1305 1065 GGUUACUGUAGCCAUAAGG 1486 1065 CCCAAGAUCCUGAAACAGA 1306 1065 CCCAAGAUCCUGAAACAGA 1306 1083 UCUGUUUCAGGAUCUUGGG 1487 1083 AGCAUGACCCUGAACCUGG 1307 1083 AGCAUGACCCUGAACCUGG 1307 1101 CCAGGUUCAGGGUCAUGCU 1488 1101 GCCGACCCAGUGGGGAGCC 1308 1101 GCCGACCCAGUGGGGAGCC 1308 1119 GGCUCCCCACUGGGUCGGC 1489 1119 CUGAAGCCGCACCUCCGCG 1309 1119 CUGAAGCCGCACCUCCGCG 1309 1137 CGCGGAGGUGCGGCUUCAG 1490 1137 GCCAAGAACUCGGACCUCC 1310 1137 GCCAAGAACUCGGACCUCC 1310 1155 GGAGGUCCGAGUUCUUGGC 1491 1155 CUCACCUCGCCCGACGUGG 1311 1155 CUCACCUCGCCCGACGUGG 1311 1173 CCACGUCGGGCGAGGUGAG 1492 1173 GGGCUGCUCAAGCUGGCGU 1312 1173 GGGCUGCUCAAGCUGGCGU 1312 1191 ACGCCAGCUUGAGCAGCCC 1493 1191 UCGCCCGAGCUGGAGCGCC 1313 1191 UCGCCCGAGCUGGAGCGCC 1313 1209 GGCGCUCCAGCUCGGGCGA 1494 1209 CUGAUAAUCCAGUCCAGCA 1314 1209 CUGAUAAUCCAGUCCAGCA 1314 1227 UGCUGGACUGGAUUAUCAG 1495 1227 AACGGGCACAUCACCACCA 1315 1227 AACGGGCACAUCACCACCA 1315 1245 UGGUGGUGAUGUGCCCGUU 1496 1245 ACGCCGACCCCCACCCAGU 1316 1245 ACGCCGACCCCCACCCAGU 1316 1263 ACUGGGUGGGGGUCGGCGU 1497 1263 UUCCUGUGCCCCAAGAACG 1317 1263 UUCCUGUGCCCCAAGAACG 1317 1281 CGUUCUUGGGGCACAGGAA 1498 1281 GUGACAGAUGAGCAGGAGG 1318 1281 GUGACAGAUGAGCAGGAGG 1318 1299 CCUCCUGCUCAUCUGUCAC 1499 1299 GGGUUCGCCGAGGGCUUCG 1319 1299 GGGUUCGCCGAGGGCUUCG 1319 1317 CGAAGCCCUCGGCGAACCC 1500 1317 GUGCGCGCCCUGGCCGAAC 1320 1317 GUGCGCGCCCUGGCCGAAC 1320 1335 GUUCGGCCAGGGCGCGCAC 1501 1335 CUGCACAGCCAGAACACGC 1321 1335 CUGCACAGCCAGAACACGC 1321 1353 GCGUGUUCUGGCUGUGCAG 1502 1353 CUGCCCAGCGUCACGUCGG 1322 1353 CUGCCCAGCGUCACGUCGG 1322 1371 CCGACGUGACGCUGGGCAG 1503 1371 GCGGCGCAGCCGGUCAACG 1323 1371 GCGGCGCAGCCGGUCAACG 1323 1389 CGUUGACCGGCUGCGCCGC 1504 1389 GGGGCAGGCAUGGUGGCUC 1324 1389 GGGGCAGGCAUGGUGGCUC 1324 1407 GAGCCACCAUGCCUGCCCC 1505 1407 CCCGCGGUAGCCUCGGUGG 1325 1407 CCCGCGGUAGCCUCGGUGG 1325 1425 CCACCGAGGCUACCGCGGG 1506 1425 GCAGGGGGCAGCGGCAGCG 1326 1425 GCAGGGGGCAGCGGCAGCG 1326 1443 CGCUGCCGCUGCCCCCUGC 1507 1443 GGCGGCUUCAGCGCCAGCC 1327 1443 GGCGGCUUCAGCGCCAGCC 1327 1461 GGCUGGCGCUGAAGCCGCC 1508 1461 CUGCACAGCGAGCCGCCGG 1328 1461 CUGCACAGCGAGCCGCCGG 1328 1479 CCGGCGGCUCGCUGUGCAG 1509 1479 GUCUACGCAAACCUCAGCA 1329 1479 GUCUACGCAAACCUCAGCA 1329 1497 UGCUGAGGUUUGCGUAGAC 1510 1497 AACUUCAACCCAGGCGCGC 1330 1497 AACUUCAACCCAGGCGCGC 1330 1515 GCGCGCCUGGGUUGAAGUU 1511 1515 CUGAGCAGCGGCGGCGGGG 1331 1515 CUGAGCAGCGGCGGCGGGG 1331 1533 CCCCGCCGCCGCUGCUCAG 1512 1533 GCGCCCUCCUACGGCGCGG 1332 1533 GCGCCCUCCUACGGCGCGG 1332 1551 CCGCGCCGUAGGAGGGCGC 1513 1551 GCCGGCCUGGCCUUUCCCG 1333 1551 GCCGGCCUGGCCUUUCCCG 1333 1569 CGGGAAAGGCCAGGCCGGC 1514 1569 GCGCAACCCCAGCAGCAGC 1334 1569 GCGCAACCCCAGCAGCAGC 1334 1587 GCUGCUGCUGGGGUUGCGC 1515 1587 CAGCAGCCGCCGCACCACC 1335 1587 CAGCAGCCGCCGCACCACC 1335 1605 GGUGGUGCGGCGGCUGCUG 1516 1605 CUGCCCCAGCAGAUGCCCG 1336 1605 CUGCCCCAGCAGAUGCCCG 1336 1623 CGGGCAUCUGCUGGGGCAG 1517 1623 GUGCAGCACCCGCGGCUGC 1337 1623 GUGCAGCACCCGCGGCUGC 1337 1641 GCAGCCGCGGGUGCUGCAC 1518 1641 CAGGCCCUGAAGGAGGAGC 1338 1641 CAGGCCCUGAAGGAGGAGC 1338 1659 GCUCCUCCUUCAGGGCCUG 1519 1659 CCUCAGACAGUGCCCGAGA 1339 1659 CCUCAGACAGUGCCCGAGA 1339 1677 UCUCGGGCACUGUCUGAGG 1520 1677 AUGCCCGGCGAGACACCGC 1340 1677 AUGCCCGGCGAGACACCGC 1340 1695 GCGGUGUCUCGCCGGGCAU 1521 1695 CCCCUGUCCCCCAUCGACA 1341 1695 CCCCUGUCCCCCAUCGACA 1341 1713 UGUCGAUGGGGGACAGGGG 1522 1713 AUGGAGUCCCAGGAGCGGA 1342 1713 AUGGAGUCCCAGGAGCGGA 1342 1731 UCCGCUCCUGGGACUCCAU 1523 1731 AUCAAGGCGGAGAGGAAGC 1343 1731 AUCAAGGCGGAGAGGAAGC 1343 1749 GCUUCCUCUCCGCCUUGAU 1524 1749 CGCAUGAGGAACCGCAUCG 1344 1749 CGCAUGAGGAACCGCAUCG 1344 1767 CGAUGCGGUUCCUCAUGCG 1525 1767 GCUGCCUCCAAGUGCCGAA 1345 1767 GCUGCCUCCAAGUGCCGAA 1345 1785 UUCGGCACUUGGAGGCAGC 1526 1785 AAAAGGAAGCUGGAGAGAA 1346 1785 AAAAGGAAGCUGGAGAGAA 1346 1803 UUCUCUCCAGCUUCCUUUU 1527 1803 AUCGCCCGGCUGGAGGAAA 1347 1803 AUCGCCCGGCUGGAGGAAA 1347 1821 UUUCCUCCAGCCGGGCGAU 1528 1821 AAAGUGAAAACCUUGAAAG 1348 1821 AAAGUGAAAACCUUGAAAG 1348 1839 CUUUCAAGGUUUUCACUUU 1529 1839 GCUCAGAACUCGGAGCUGG 1349 1839 GCUCAGAACUCGGAGCUGG 1349 1857 CCAGCUCCGAGUUCUGAGC 1530 1857 GCGUCCACGGCCAACAUGC 1350 1857 GCGUCCACGGCCAACAUGC 1350 1875 GCAUGUUGGCCGUGGACGC 1531 1875 CUCAGGGAACAGGUGGCAC 1351 1875 CUCAGGGAACAGGUGGCAC 1351 1893 GUGCCACCUGUUCCCUGAG 1532 1893 CAGCUUAAACAGAAAGUCA 1352 1893 CAGCUUAAACAGAAAGUCA 1352 1911 UGACUUUCUGUUUAAGCUG 1533 1911 AUGAACCACGUUAACAGUG 1353 1911 AUGAACCACGUUAACAGUG 1353 1929 CACUGUUAACGUGGUUCAU 1534 1929 GGGUGCCAACUCAUGCUAA 1354 1929 GGGUGCCAACUCAUGCUAA 1354 1947 UUAGCAUGAGUUGGCACCC 1535 1947 ACGCAGCAGUUGCAAACAU 1355 1947 ACGCAGCAGUUGCAAACAU 1355 1965 AUGUUUGCAACUGCUGCGU 1536 1965 UUUUGAAGAGAGACCGUCG 1356 1965 UUUUGAAGAGAGACCGUCG 1356 1983 CGACGGUCUCUCUUCAAAA 1537 1983 GGGGGCUGAGGGGCAACGA 1357 1983 GGGGGCUGAGGGGCAACGA 1357 2001 UCGUUGCCCCUCAGCCCCC 1538 2001 AAGAAAAAAAAUAACACAG 1358 2001 AAGAAAAAAAAUAACACAG 1358 2019 CUGUGUUAUUUUUUUUCUU 1539 2019 GAGAGACAGACUUGAGAAC 1359 2019 GAGAGACAGACUUGAGAAC 1359 2037 GUUCUCAAGUCUGUCUCUC 1540 2037 CUUGACAAGUUGCGACGGA 1360 2037 CUUGACAAGUUGCGACGGA 1360 2055 UCCGUCGCAACUUGUCAAG 1541 2055 AGAGAAAAAAGAAGUGUCC 1361 2055 AGAGAAAAAAGAAGUGUCC 1361 2073 GGACACUUCUUUUUUCUCU 1542 2073 CGAGAACUAAAGCCAAGGG 1362 2073 CGAGAACUAAAGCCAAGGG 1362 2091 CCCUUGGCUUUAGUUCUCG 1543 2091 GUAUCCAAGUUGGACUGGG 1363 2091 GUAUCCAAGUUGGACUGGG 1363 2109 CCCAGUCCAACUUGGAUAC 1544 2109 GUUCGGUCUGACGGCGCCC 1364 2109 GUUCGGUCUGACGGCGCCC 1364 2127 GGGCGCCGUCAGACCGAAC 1545 2127 CCCAGUGUGCACGAGUGGG 1365 2127 CCCAGUGUGCACGAGUGGG 1365 2145 CCCACUCGUGCACACUGGG 1546 2145 GAAGGACUUGGUCGCGCCC 1366 2145 GAAGGACUUGGUCGCGCCC 1366 2163 GGGCGCGACCAAGUCCUUC 1547 2163 CUCCCUUGGCGUGGAGCCA 1367 2163 CUCCCUUGGCGUGGAGCCA 1367 2181 UGGCUCCACGCCAAGGGAG 1548 2181 AGGGAGCGGCCGCCUGCGG 1368 2181 AGGGAGCGGCCGCCUGCGG 1368 2199 CCGCAGGCGGCCGCUCCCU 1549 2199 GGCUGCCCCGCUUUGCGGA 1369 2199 GGCUGCCCCGCUUUGCGGA 1369 2217 UCCGCAAAGCGGGGCAGCC 1550 2217 ACGGGCUGUCCCCGCGCGA 1370 2217 ACGGGCUGUCCCCGCGCGA 1370 2235 UCGCGCGGGGACAGCCCGU 1551 2235 AACGGAACGUUGGACUUUC 1371 2235 AACGGAACGUUGGACUUUC 1371 2253 GAAAGUCCAACGUUCCGUU 1552 2253 CGUUAACAUUGACCAAGAA 1372 2253 CGUUAACAUUGACCAAGAA 1372 2271 UUCUUGGUCAAUGUUAACG 1553 2271 ACUGCAUGGACCUAACAUU 1373 2271 ACUGCAUGGACCUAACAUU 1373 2289 AAUGUUAGGUCCAUGCAGU 1554 2289 UCGAUCUCAUUCAGUAUUA 1374 2289 UCGAUCUCAUUCAGUAUUA 1374 2307 UAAUACUGAAUGAGAUCGA 1555 2307 AAAGGGGGGAGGGGGAGGG 1375 2307 AAAGGGGGGAGGGGGAGGG 1375 2325 CCCUCCCCCUCCCCCCUUU 1556 2325 GGGUUACAAACUGCAAUAG 1376 2325 GGGUUACAAACUGCAAUAG 1376 2343 CUAUUGCAGUUUGUAACCC 1557 2343 GAGACUGUAGAUUGCUUCU 1377 2343 GAGACUGUAGAUUGCUUCU 1377 2361 AGAAGCAAUCUACAGUCUC 1558 2361 UGUAGUACUCCUUAAGAAC 1378 2361 UGUAGUACUCCUUAAGAAC 1378 2379 GUUCUUAAGGAGUACUACA 1559 2379 CACAAAGCGGGGGGAGGGU 1379 2379 CACAAAGCGGGGGGAGGGU 1379 2397 ACCCUCCCCCCGCUUUGUG 1560 2397 UUGGGGAGGGGCGGCAGGA 1380 2397 UUGGGGAGGGGCGGCAGGA 1380 2415 UCCUGCCGCCCCUCCCCAA 1561 2415 AGGGAGGUUUGUGAGAGCG 1381 2415 AGGGAGGUUUGUGAGAGCG 1381 2433 CGCUCUCACAAACCUCCCU 1562 2433 GAGGCUGAGCCUACAGAUG 1382 2433 GAGGCUGAGCCUACAGAUG 1382 2451 CAUCUGUAGGCUCAGCCUC 1563 2451 GAACUCUUUCUGGCCUGCU 1383 2451 GAACUCUUUCUGGCCUGCU 1383 2469 AGCAGGCCAGAAAGAGUUC 1564 2469 UUUCGUUAACUGUGUAUGU 1384 2469 UUUCGUUAACUGUGUAUGU 1384 2487 ACAUACACAGUUAACGAAA 1565 2487 UACAUAUAUAUAUUUUUUA 1385 2487 UACAUAUAUAUAUUUUUUA 1385 2505 UAAAAAAUAUAUAUAUGUA 1566 2505 AAUUUGAUUAAAGCUGAUU 1386 2505 AAUUUGAUUAAAGCUGAUU 1386 2523 AAUCAGCUUUAAUCAAAUU 1567 2523 UACUGUCAAUAAACAGCUU 1387 2523 UACUGUCAAUAAACAGCUU 1387 2541 AAGCUGUUUAUUGACAGUA 1568 2541 UCAUGCCUUUGUAAGUUAU 1388 2541 UCAUGCCUUUGUAAGUUAU 1388 2559 AUAACUUACAAAGGCAUGA 1569 2559 UUUCUUGUUUGUUUGUUUG 1389 2559 UUUCUUGUUUGUUUGUUUG 1389 2577 CAAACAAACAAACAAGAAA 1570 2577 GGGUAUCCUGCCCAGUGUU 1390 2577 GGGUAUCCUGCCCAGUGUU 1390 2595 AACACUGGGCAGGAUACCC 1571 2595 UGUUUGUAAAUAAGAGAUU 1391 2595 UGUUUGUAAAUAAGAGAUU 1391 2613 AAUCUCUUAUUUACAAACA 1572 2613 UUGGAGCACUCUGAGUUUA 1392 2613 UUGGAGCACUCUGAGUUUA 1392 2631 UAAACUCAGAGUGCUCCAA 1573 2631 ACCAUUUGUAAUAAAGUAU 1393 2631 ACCAUUUGUAAUAAAGUAU 1393 2649 AUACUUUAUUACAAAUGGU 1574 2649 UAUAAUUUUUUUAUGUUUU 1394 2649 UAUAAUUUUUUUAUGUUUU 1394 2667 AAAACAUAAAAAAAUUAUA 1575 2667 UGUUUCUGAAAAUUCCAGA 1395 2667 UGUUUCUGAAAAUUCCAGA 1395 2685 UCUGGAAUUUUCAGAAACA 1576 2685 AAAGGAUAUUUAAGAAAAU 1396 2685 AAAGGAUAUUUAAGAAAAU 1396 2703 AUUUUCUUAAAUAUCCUUU 1577 2703 UACAAUAAACUAUUGGAAA 1397 2703 UACAAUAAACUAUUGGAAA 1397 2721 UUUCCAAUAGUUUAUUGUA 1578 2721 AGUACUCCCCUAACCUCUU 1398 2721 AGUACUCCCCUAACCUCUU 1398 2739 AAGAGGUUAGGGGAGUACU 1579 2739 UUUCUGCAUCAUCUGUAGA 1399 2739 UUUCUGCAUCAUCUGUAGA 1399 2757 UCUACAGAUGAUGCAGAAA 1580 2757 AUCCUAGUCUAUCUAGGUG 1400 2757 AUCCUAGUCUAUCUAGGUG 1400 2775 CACCUAGAUAGACUAGGAU 1581 2775 GGAGUUGAAAGAGUUAAGA 1401 2775 GGAGUUGAAAGAGUUAAGA 1401 2793 UCUUAACUCUUUCAACUCC 1582 2793 AAUGCUCGAUAAAAUCACU 1402 2793 AAUGCUCGAUAAAAUCACU 1402 2811 AGUGAUUUUAUCGAGCAUU 1583 2811 UCUCAGUGCUUCUUACUAU 1403 2811 UCUCAGUGCUUCUUACUAU 1403 2829 AUAGUAAGAAGCACUGAGA 1584 2829 UUAAGCAGUAAAAACUGUU 1404 2829 UUAAGCAGUAAAAACUGUU 1404 2847 AACAGUUUUUACUGCUUAA 1585 2847 UCUCUAUUAGACUUAGAAA 1405 2847 UCUCUAUUAGACUUAGAAA 1405 2865 UUUCUAAGUCUAAUAGAGA 1586 2865 AUAAAUGUACCUGAUGUAC 1406 2865 AUAAAUGUACCUGAUGUAC 1406 2883 GUACAUCAGGUACAUUUAU 1587 2883 CCUGAUGCUAUGUCAGGCU 1407 2883 CCUGAUGCUAUGUCAGGCU 1407 2901 AGCCUGACAUAGCAUCAGG 1588 2901 UUCAUACUCCACGCUCCCC 1408 2901 UUCAUACUCCACGCUCCCC 1408 2919 GGGGAGCGUGGAGUAUGAA 1589 2919 CCAGCGUAUCUAUAUGGAA 1409 2919 CCAGCGUAUCUAUAUGGAA 1409 2937 UUCCAUAUAGAUACGCUGG 1590 2937 AUUGCUUACCAAAGGCUAG 1410 2937 AUUGCUUACCAAAGGCUAG 1410 2955 CUAGCCUUUGGUAAGCAAU 1591 2955 GUGCGAUGUUUCAGGAGGC 1411 2955 GUGCGAUGUUUCAGGAGGC 1411 2973 GCCUCCUGAAACAUCGCAC 1592 2973 CUGGAGGAAGGGGGGUUGC 1412 2973 CUGGAGGAAGGGGGGUUGC 1412 2991 GCAACCCCCCUUCCUCCAG 1593 2991 CAGUGGAGAGGGACAGCCC 1413 2991 CAGUGGAGAGGGACAGCCC 1413 3009 GGGCUGUCCCUCUCCACUG 1594 3009 CACUGAGAAGUCAAACAUU 1414 3009 CACUGAGAAGUCAAACAUU 1414 3027 AAUGUUUGACUUCUCAGUG 1595 3027 UUCAAAGUUUGGAUUGCAU 1415 3027 UUCAAAGUUUGGAUUGCAU 1415 3045 AUGCAAUCCAAACUUUGAA 1596 3045 UCAAGUGGCAUGUGCUGUG 1416 3045 UCAAGUGGCAUGUGCUGUG 1416 3063 CACAGCACAUGCCACUUGA 1597 3063 GACCAUUUAUAAUGUUAGA 1417 3063 GACCAUUUAUAAUGUUAGA 1417 3081 UCUAACAUUAUAAAUGGUC 1598 3081 AAAUUUUACAAUAGGUGCU 1418 3081 AAAUUUUACAAUAGGUGCU 1418 3099 AGCACCUAUUGUAAAAUUU 1599 3099 UUAUUCUCAAAGCAGGAAU 1419 3099 UUAUUCUCAAAGCAGGAAU 1419 3117 AUUCCUGCUUUGAGAAUAA 1600 3117 UUGGUGGCAGAUUUUACAA 1420 3117 UUGGUGGCAGAUUUUACAA 1420 3135 UUGUAAAAUCUGCCACCAA 1601 3135 AAAGAUGUAUCCUUCCAAU 1421 3135 AAAGAUGUAUCCUUCCAAU 1421 3153 AUUGGAAGGAUACAUCUUU 1602 3153 UUUGGAAUCUUCUCUUUGA 1422 3153 UUUGGAAUCUUCUCUUUGA 1422 3171 UCAAAGAGAAGAUUCCAAA 1603 3171 ACAAUUCCUAGAUAAAAAG 1423 3171 ACAAUUCCUAGAUAAAAAG 1423 3189 CUUUUUAUCUAGGAAUUGU 1604 3189 GAUGGCCUUUGUCUUAUGA 1424 3189 GAUGGCCUUUGUCUUAUGA 1424 3207 UCAUAAGACAAAGGCCAUC 1605 3207 AAUAUUUAUAACAGCAUUC 1425 3207 AAUAUUUAUAACAGCAUUC 1425 3225 GAAUGCUGUUAUAAAUAUU 1606 3225 CUGUCACAAUAAAUGUAUU 1426 3225 CUGUCACAAUAAAUGUAUU 1426 3243 AAUACAUUUAUUGUGACAG 1607 3234 UAAAUGUAUUCAAAUACCA 1427 3234 UAAAUGUAUUCAAAUACCA 1427 3252 UGGUAUUUGAAUACAUUUA 1608 The 3-ends of the Upper sequence and the Lower sequence of the siNA construct can include an overhang sequence, for example about 1, 2, 3, or 4 nucleotides in length, preferably 2 nucleotides in length, wherein the overhanging sequence of the lower sequence is optionally complementary to a portion of the target sequence. The upper sequence is also referred to as the sense strand, whereas the lower sequence is also referred to as the antisense strand. The upper and lower sequences in the Table can further comprise a chemical modification having Formulae I-VII or any combination thereof.

TABLE III MAP Kinase Synthetic Modified siNA constructs Target Seq Seq Pos Target ID Aliases Sequence ID MAPK1/ERK2 3302 ACCAGACCUACUGCCAGAGAACC 1113 MAPK1:424U21 siRNA sense CAGACCUACUGCCAGAGAATT 1129 3852 AUCACACAGGGUUCCUGACAGAA 1114 MAPK1:778U21 siRNA sense CACACAGGGUUCCUGACAGTT 1130 3892 UUGGCUCUAGUCACUGGCAUCUC 1115 MAPK1:1718U21 siRNA sense GGCUCUAGUCACUGGCAUCTT 1131 3946 ACUGUGGAGUUGACUCGGUGUUC 1116 MAPK1:2525U21 siRNA sense UGUGGAGUUGACUCGGUGUTT 1132 3302 ACCAGACCUACUGCCAGAGAACC 1113 MAPK1:442L21 siRNA (424C) UUCUCUGGCAGUAGGUCUGTT 1133 antisense 3852 AUCACACAGGGUUCCUGACAGAA 1114 MAPK1:796L21 siRNA (778C) CUGUCAGGAACCCUGUGUGTT 1134 antisense 3892 UUGGCUCUAGUCACUGGCAUCUC 1115 MAPK1:1736L21 siRNA (1718C) GAUGCCAGUGACUAGAGCCTT 1135 antisense 3946 ACUGUGGAGUUGACUCGGUGUUC 1116 MAPK1:2543L21 siRNA (2525C) ACACCGAGUCAACUCCACATT 1136 antisense 3302 ACCAGACCUACUGCCAGAGAACC 1113 MAPK1:424U21 siRNA stab04 B cAGAccuAcuGccAGAGAATT B 1137 sense RPI 30817 3852 AUCACACAGGGUUCCUGACAGAA 1114 MAPK1:778U21 siRNA stab04 B cAcAcAGGGuuccuGAcAGTT B 1138 sense RPI 30818 3892 UUGGCUCUAGUCACUGGCAUCUC 1115 MAPK1:1718U21 siRNA stab04 B GGcucuAGucAcuGGcAucTT B 1139 sense RPI 30819 3946 ACUGUGGAGUUGACUCGGUGUUC 1116 MAPK1:2525U21 siRNA stab04 B uGuGGAGuuGAcucGGuGuTT B 1140 sense RPI 30820 3302 ACCAGACCUACUGCCAGAGAACC 1113 MAPK1:442L21 siRNA (424C) uucucuGGcAGuAGGucuGTsT 1141 stab05 antisense RPI 30821 3852 AUCACACAGGGUUCCUGACAGAA 1114 MAPK1:796L21 siRNA (778C) cuGucAGGAAcccuGuGuGTsT 1142 stab05 antisense RPI 30822 3892 UUGGCUCUAGUCACUGGCAUCUC 1115 MAPK1:1736L21 siRNA (1718C) GAuGccAGuGAcuAGAGccTsT 1143 stab05 antisense RPI 30823 3946 ACUGUGGAGUUGACUCGGUGUUC 1116 MAPK1:2543L21 siRNA (2525C) AcAccGAGucAAcuCCAcATsT 1144 stab05 antisense RPI 30824 3302 ACCAGACCUA0UGCCAGAGAACC 1113 MARK1:424U21 siRNA stab07 B cAGAccuAcuGccAGAGAATT B 1145 sense 3852 AUCACACAGGGUUCCUGACAGAA 1114 MARK1:778U21 siRNA stabo7 B cAcAcAGGGuuccuGAcAGTT B 1146 sense 3892 UUGGCUCUAGUCACUGGCAUCUC 1115 MAPK1:1718U21 siRNA stabo7 B GGcucuAGucAcuGGcAucTTB 1147 sense 3946 ACUGUGGAGUUGACUCGGUGUUC 1116 MARK1:2525U21 siRNA stabo7 B uGuGGAGuuGAcucGGuGuTT B 1148 sense 3302 ACCAGACCUACUGCCAGAGAACC 1113 MARK1:442L21 siRNA (424C) uucucuGGcAGuAGGucuGTsT 1149 stab11 antisense 3852 AUCACACAGGGUUCCUGACAGAA 1114 MARK1:796L21 siRNA (778C) cuGucAGGAAcccuGuGuGTsT 1150 stab11 antisense 3892 UUGGCUCUAGUCACUGGCAUCUC 1115 MARK1:1736L21 siRNA (1718C) GAuGccAGuGAcuAGAGccTsT 1151 stab11 antisense 3946 ACUGUGGAGUUGACUCGGUGUUC 1116 MARK1:2543L21 siRNA (25250) AcAccGAGucAAcuccAcATsT 1152 stab11 antisense Target Seq Seq Pos Target ID Aliases Sequence ID MAPK3/ERK1 283 CCUUCGAACAUCAGACCUACUGC 1117 MAPK3:285U21 siRNA sense UUCGAACAUCAGACCUACUTT 1153 709 UGAACUCCAAGGGCUAUACCAAG 1118 MAPK3:711U21 siRNA sense AACUCCAAGGGCUAUACCATT 1154 718 AGGGCUAUACCAAGUCCAUCGAC 1119 MAPK3:720U21 siRNA sense GGCUAUACCAAGUCCAUCGTT 1155 1778 UUCUGUGUGUGGUGAGCAGAAGU 1120 MAPK3:1780U21 siRNA sense CUGUGUGUGGUGAGCAGAATT 1156 283 CCUUCGAACAUCAGACCUACUGC 1117 MAPK3:303L21 siRNA (285C) AGUAGGUCUGAUGUUCGAATT 1157 antisense 709 UGAACUCCAAGGGCUAUACCAAG 1118 MAPK3:729L21 siRNA (711C) UGGUAUAGCCCUUGGAGUUTT 1158 antisense 718 AGGGCUAUACCAAGUCCAUCGAC 1119 MAPK3:738L21 siRNA (720C) CGAUGGACUUGGUAUAGCCTT 1159 antisense 1778 UUCUGUGUGUGGUGAGCAGAAGU 1120 MAPK3:1798L21 siRNA (1780C) UUCUGCUCACCACACACAGTT 1160 antisense 283 CCUUCGAACAUCAGACCUACUGC 1117 MAPK3:285U21 siRNA stab04 sense B uucGAAcAucAGAccuAcuTT B 1161 709 UGAACUCCAAGGGCUAUACCAAG 1118 MAPK3:711U21 siRNA stab04 sense B AAcuccAAGGGcuAuAccATT B 1162 718 AGGGCUAUACCAAGUCCAUCGAC 1119 MAPK3:720U21 siRNA stab04 sense B GGcuAuAccAAGuccAucGTT B 1163 1778 UUCUGUGUGUGGUGAGCAGAAGU 1120 MAPK3:1780U21 siRNA stab04 sense B cuGuGuGuGGuGAGcAGAATT B 1164 283 CCUUCGAACAUCAGACCUACUGC 1117 MAPK3:303L21 siRNA (285C) stab05 AGuAGGucuGAuGuucGAATsT 1165 antisense 709 UGAACUCCAAGGGCUAUACCAAG 1118 MAPK3:729L21 siRNA (711C) stab05 uGGuAuAGcccuuGGAGuuTsT 1166 antisense 718 AGGGCUAUACCAAGUCCAUCGAC 1119 MAPK3:738L21 siRNA (720C) stab05 cGAuGGAcuuGGuAuAGccTsT 1167 antisense 1778 UUCUGUGUGUGGUGAGCAGAAGU 1120 MAPK3:1798L21 siRNA (1780C) uucuGcucAccAcAcAcAGTsT 1168 stab05 antisense 283 CCUUCGAACAUCAGACCUACUGC 1117 MAPK3:285U21 siRNA stab07 sense B uucGAAcAucAGAccuAcuTT B 1169 709 UGAACUCCAAGGGCUAUACCAAG 1118 MAPK3:711U21 siRNA stab07 sense B AAcuccAAGGGcuAuAccATT B 1170 718 AGGGCUAUACCAAGUCCAUCGAC 1119 MAPK3:720U21 siRNA stab07 sense B GGcuAuAccAAGuccAucGTT B 1171 1778 UUCUGUGUGUGGUGAGCAGAAGU 1120 MAPK3:1780U21 siRNA stab07 sense B cuGuGuGuGGuGAGcAGAATT B 1172 283 CCUUCGAACAUCAGACCUACUGC 1117 MAPK3:303L21 siRNA (285C) stab11 AGuAGGucuGAuGuucGAATsT 1173 antisense 709 UGAACUCCAAGGGCUAUACCAAG 1118 MAPK3:729L21 siRNA (711C) stab11 uGGuAuAGcccuuGGAGuuTsT 1174 antisense 718 AGGGCUAUACCAAGUCCAUCGAC 1119 MAPK3:738L21 siRNA (720C) stab11 cGAuGGAcuuGGuAuAGccTsT 1175 antisense 1778 UUCUGUGUGUGGUGAGCAGAAGU 1120 MAPK3:1798L21 siRNA (178C0) uucuGcucAccAcAcAcAGTsT 1176 stab11 antisense Target Seq Seq Pos Target ID RPI # Aliases Sequence ID MAPK8/JNK1 733 AACAGCUUGGAACACCAUGUCCU 1121 31517 MAPK8:735U21 siRNA sense CAGCUUGGAACACCAUGUCTT 1177 853 UUUUCCCAGCUGACUCAGAACAC 1122 31518 MAPK8:855U21 siRNA sense UUCCCAGCUGACUCAGAACTT 1178 1224 CAAUGUCAACAGAUCCGACUUUG 1123 31519 MAPK8:1226U21 siRNA sense AUGUCAACAGAUCCGACUUTT 1179 1242 CUUUGGCCUCUGAUACAGACAGC 1124 31520 MAPK8:1244U21 siRNA sense UUGGCCUCUGAUACAGACATT 1180 733 AACAGCUUGGAACACCAUGUCCU 1121 31521 MAPK8:753L21 siRNA (735C) GACAUGGUGUUCCAAGCUGTT 1181 antisense 853 UUUUCCCAGCUGACUCAGAACAC 1122 31522 MAPK8:873L21 siRNA (855C) GUUCUGAGUCAGCUGGGAATT 1182 antisense 1224 CAAUGUCAACAGAUCCGACUUUG 1123 31523 MAPK8:1244L21 siRNA (1226C) AAGUCGGAUCUGUUGACAUTT 1183 antisense 1242 CUUUGGCCUCUGAUACAGACAGC 1124 31524 MAPK8:1262L21 siRNA (1244C) UGUCUGUAUCAGAGGCCAATT 1184 antisense 733 AACAGCUUGGAACACCAUGUCCU 1121 MAPK8:735U21 siRNA stab4 B cAGcuuGGAAcAccAuGucTT B 1185 sense 853 UUUUCCCAGCUGACUCAGAACAC 1122 MAPK8:855U21 siRNA stab4 B uucccAGcuGAcucAGAAcTT B 1186 sense 1224 CAAUGUCAACAGAUCCGACUUUG 1123 MAPK8:1226U21 siRNA stab4 BAuGucAAcAGAuccGAcuuTTB 1187 sense 1242 CUUUGGCCUCUGAUACAGACAGC 1124 MAPK8:1244U21 siRNA stab4 B uuGGccucuGAuAcAGAcATT B 1188 sense 733 AACAGCUUGGAACACCAUGUCCU 1121 MAPK8:753L21 siRNA (735C) GAcAuGGuGuuccAAGcuGTsT 1189 stab5 antisense 853 UUUUCCCAGCUGACUCAGAACAC 1122 MAPK8:873L21 siRNA (855C) GuucuGAGucAGcuGGGAATsT 1190 stab5 antisense 1224 CAAUGUCAACAGAUCCGACUUUG 1123 MAPK8:1244L21 siRNA (1226C) AAGucGGAucuGuuGAcAuTsT 1191 stab5 antisense 1242 CUUUGGCCUCUGAUACAGACAGC 1124 MAPK8:1262L21 siRNA (1244C) uGucuGuAucAGAGGccAATsT 1192 stab5 antisense 733 AACAGCUUGGAACACCAUGUCCU 1121 MAPK8:735U21 siRNA stab7 BcAGcuuGGAAcAccAuGucTTB 1193 sense 853 UUUUCCCAGCUGACUCAGAACAC 1122 MAPK8:855U21 siRNA stab7 B uucccAGcuGAcucAGAAcTT B 1194 sense 1224 CAAUGUCAACAGAUCCGACUUUG 1123 MAPK8:1226U21 siRNA stab7 B AuGucAAcAGAuccGAcuuTT B 1195 sense 1242 CUUUGGCCUCUGAUACAGACAGC 1124 MAPK8:1244U21 siRNA stab7 B uuGGccucuGAuAcAGAcATT B 1196 sense 733 AACAGCUUGGAACACCAUGUCCU 1121 MAPK8:753L21 siRNA (735C) GAcAuGGuGuuccAAGcuGTsT 1197 stab11 antisense 853 UUUUCCCAGCUGACUCAGAACAC 1122 MAPK8:873L21 siRNA (855C) GuucuGAGucAGcuGGGAATsT 1198 stab11 antisense 1224 CAAUGUCAACAGAUCCGACUUUG 1123 MAPK8:1244L21 siRNA (1226C) AAGucGGAucuGuuGAcAuTsT 1199 stab11 antisense 1242 CUUUGGCCUCUGAUACAGACAGC 1124 MAPK8:1262L21 siRNA (1244C) uGucuGuAucAGAGGccAATsT 1200 stab11 antisense Target Seq Pos Target ID RPI # Aliases Sequence ID MAPK14/p38 1278 GCCUACUUUGCUCAGUACCACGA 1125 31586 MAPK14:1280U21 siRNA sense CUACUUUGCUCAGUACCACTT 1201 1609 UGUCUGUCUUUGUGGGAGGGUAA 1126 31587 MARK14:1611U21 siRNA sense UCUGUCUUUGUGGGAGGGUTT 1202 2882 AAAAGGGUCUUCUUGGCAGCUUA 1127 31588 MAPK14:2884U21 siRNA sense AAGGGUCUUCUUGGCAGCUTT 1203 3554 GGACUCUAAGCUGGAGCUCUUGG 1128 31589 MAPK14:3556U21 siRNA sense ACUCUAAGCUGGAGCUCUUTT 1204 1278 GCCUACUUUGCUCAGUACCACGA 1125 31590 MAPK14:1298L21 siRNA (1280C) GUGGUACUGAGCAAAGUAGTT 1205 antisense 1609 UGUCUGUCUUUGUGGGAGGGUAA 1126 31591 MAPK14:1629L21 siRNA (1611C) ACCCUCCCACAAAGACAGATT 1206 antisense 2882 AAAAGGGUCUUCUUGGCAGCUUA 1127 31592 MARK14:2902L21 siRNA (2884C) AGCUGCCAAGAAGACCCUUTT 1207 antisense 3554 GGACUCUAAGCUGGAGCUCUUGG 1128 31593 MAPK14:3574L21 siRNA (3556C) AAGAGCUCCAGCUUAGAGUTT 1208 antisense 1278 GCCUACUUUGCUCAGUACCACGA 1125 MAPK14:1280U21 siRNA stab04 B cuAcuuuGcucAGuAccAcTT B 1209 sense 1609 UGUCUGUCUUUGUGGGAGGGUAA 1126 MARK14:1611U21 siRNA stab04 B ucuGucuuuGuGGGAGGGuTT B 1210 sense 2882 AAAAGGGUCUUCUUGGCAGCUUA 1127 MAPK14:2884U21 siRNA stab04 B AAGGGucuucuuGGcAGcuTT B 1211 sense 3554 GGACUCUAAGCUGGAGCUCUUGG 1128 MAPK14:3556U21 siRNA stab04 B AcucuAAGcuGGAGcucuuTT B 1212 sense 1278 GCCUACUUUGCUCAGUACCACGA 1125 MAPK14:1298L21 siRNA (1280C) GuGGuAcuGAGcAAAGuAGTsT 1213 stab05 antisense 1609 UGUCUGUCUUUGUGGGAGGGUAA 1126 MARK14:1629L21 siRNA (1611C) AcccucccAcAAAGAcAGATsT 1214 stab05 antisense 2882 AAAAGGGUCUUCUUGGCAGCUUA 1127 MAPK14:2902L21 siRNA (2884C) AGcuGccAAGAAGAcccuuTsT 1215 stab05 antisense 3554 GGACUCUAAGCUGGAGCUCUUGG 1128 MARK14:3574L21 siRNA (3556C) AAGAGcuccAGcuuAGAGuTsT 1216 stab05 antisense 1278 GCCUACUUUGCUCAGUACCACGA 1125 MAPK14:1280U21 siRNA stab07 B cuAcuuuGcucAGuAccAcTT B 1217 sense 1609 UGUCUGUCUUUGUGGGAGGGUAA 1126 MARK14:1611U21 siRNA stab07 B ucuGucuuuGuGGGAGGGuTT B 1218 sense 2882 AAAAGGGUCUUCUUGGCAGCUUA 1127 MAPK14:2884U21 siRNA stab07 B AAGGGucuucuuGGcAGcuTT B 1219 sense 3554 GGACUCUAAGCUGGAGCUCUUGG 1128 MAPK14:3556U21 siRNA stab07 B AcucuAAGcuGGAGcucuuTT B 1220 sense 1278 GCCUACUUUGCUCAGUACCACGA 1125 MAPK14:1298L21 siRNA (1280C) GuGGuAcuGAGcAAAGuAGTsT 1221 stab11 antisense 1609 UGUCUGUCUUUGUGGGAGGGUAA 1126 MARK14:1629L21 siRNA (1611C) AcccucccAcAAAGAcAGATsT 1222 stab11 antisense 2882 AAAAGGGUCUUCUUGGCAGCUUA 1127 MAPK14:2902L21 siRNA (2884C) AGcuGccAAGAAGAcccuuTsT 1223 stab11 antisense 3554 GGACUCUAAGCUGGAGCUCUUGG 1128 MAPK14:3574L21 siRNA (3556C) AAGAGcuccAGcuuAGAGuTsT 1224 stab11 antisense Target Seq Seq Pos Target ID RPI# Aliases Sequence ID c-JUN 1817 GGAAAAAGUGAAAACCUUGAAAG 1609 JUN:1819U21 siRNA sense AAAAAGUGAAAACCUUGAATT 1617 1935 CAACUCAUGCUAACGCAGCAGUU 1610 JUN:1937U21 siRNA sense ACUCAUGCUAACGCAGCAGTT 1618 2259 CAUUGACCAAGAACUGCAUGGAC 1611 JUN:2261U21 siRNA sense UUGACCAAGAACUGCAUGGTT 1619 2264 ACCAAGAACUGCAUGGACCUAAC 1612 JUN:2266U21 siRNA sense CAAGAACUGCAUGGACCUATT 1620 2269 GAACUGCAUGGACCUAACAUUCG 1613 JUN:2271U21 siRNA sense ACUGCAUGGACCUAACAUUTT 1621 2270 AACUGCAUGGACCUAACAUUCGA 1614 JUN:2272U21 siRNA sense CUGCAUGGACCUAACAUUCTT 1622 2272 CUGCAUGGACCUAACAUUCGAUC 1615 JUN:2274U21 siRNA sense GCAUGGACCUAACAUUCGATT 1623 2274 GCAUGGACCUAACAUUCGAUCUC 1616 JUN:2276U21 siRNA sense AUGGACCUAACAUUCGAUCTT 1624 1817 GGAAAAAGUGAAAACCUUGAAAG 1609 JUN:1837L21 siRNA (1819C) UUCAAGGUUUUCACUUUUUTT 1625 antisense 1935 CAACUCAUGCUAACGCAGCAGUU 1610 JUN:1955L21 siRNA (1937C) CUGCUGCGUUAGCAUGAGUTT 1626 antisense 2259 CAUUGACCAAGAACUGCAUGGAC 1611 JUN:2279L21 siRNA (2261C) CCAUGCAGUUCUUGGUCAATT 1627 antisense 2264 ACCAAGAACUGCAUGGACCUAAC 1612 JUN:2284L21 siRNA (2266C) UAGGUCCAUGCAGUUCUUGTT 1628 antisense 2269 GAACUGCAUGGACCUAACAUUCG 1613 JUN:2289L21 siRNA (2271C) AAUGUUAGGUCCAUGCAGUTT 1629 antisense 2270 AACUGCAUGGACCUAACAUUCGA 1614 JUN:2290L21 siRNA (2272C) GAAUGUUAGGUCCAUGCAGTT 1630 antisense 2272 CUGCAUGGACCUAACAUUCGAUC 1615 JUN:2292L21 siRNA (2274C) UCGAAUGUUAGGUCCAUGCTT 1631 antisense 2274 GCAUGGACCUAACAUUCGAUCUC 1616 JUN:2294L21 siRNA (2276C) GAUCGAAUGUUAGGUCCAUTT 1632 antisense 1817 GGAAAAAGUGAAAACCUUGAAAG 1609 JUN:1819U21 siRNA stab04 B AAAAAGuGAAAAccuuGAATT B 1633 sense 1935 CAACUGAUGCUAACGCAGCAGUU 1610 JUN:1937U21 siRNA stab04 B AcucAuGcuAAcGcAGcAGTT B 1634 sense 2259 CAUUGACCAAGAACUGCAUGGAC 1611 JUN:2261U21 siRNA stab04 B uuGAccAAGAAcuGcAuGGTT B 1635 sense 2264 ACCAAGAACUGCAUGGACCUAAC 1612 JUN:2266U21 siRNA stab04 B cAAGAAcuGcAuGGAccuATT B 1636 sense 2269 GAACUGCAUGGACCUAACAUUCG 1613 JUN:2271U21 siRNA stab04 B AcuGcAuGGAccuAAcAuuTT B 1637 sense 2270 AACUGCAUGGACCUAACAUUCGA 1614 JUN:2272U21 siRNA stab04 B cuGcAuGGAccuAAcAuucTT B 1638 sense 2272 CUGCAUGGACCUAACAUUCGAUC 1615 JUN:2274U21 siRNA stab04 B GcAuGGAccuAAcAuucGATT B 1639 sense 2274 GCAUGGACCUAACAUUCGAUCUC 1616 JUN:2276U21 siRNA stab04 B AuGGAccuAAcAuucGAucTT B 1640 sense 1817 GGAAAAAGUGAAAACCUUGAAAG 1609 JUN:1837L21 siRNA (1819C) uucAAGGuuuucAcuuuuuTsT 1641 stab05 antisense 1935 CAACUCAUGCUAACGCAGCAGUU 1610 JUN:1955L21 siRNA (1937C) cuGcuGcGuuAGcAuGAGuTsT 1642 stab05 antisense 2259 CAUUGACCAAGAACUGCAUGGAC 1611 JUN:2279L21 siRNA (2261C) ccAuGcAGuucuuGGucAATsT 1643 stab05 antisense 2264 ACCAAGAACUGCAUGGACCUAAC 1612 JUN:2284L21 siRNA (2266C) uAGGuccAuGcAGuucuuGTsT 1644 stab05 antisense 2269 GAACUGCAUGGACCUAACAUUCG 1613 JUN:2289L21 siRNA (2271C) AAuGuuAGGuccAuGcAGuTsT 1645 stab05 antisense 2270 AACUGCAUGGACCUAACAUUCGA 1614 JUN:2290L21 siRNA (2272C) GAAuGuuAGGuccAuGcAGTsT 1646 stab05 antisense 2272 CUGCAUGGACCUAACAUUCGAUC 1615 JUN:2292L21 siRNA (2274C) ucGAAuGuuAGGuccAuGcTsT 1647 stab05 antisense 2274 GCAUGGACCUAACAUUCGAUCUG 1616 JUN:2294L21 siRNA (2276C) GAucGAAuGuuAGGuccAuTsT 1648 stab05 antisense 1817 GGAAAAAGUGAAAACCUUGAAAG 1609 31818 JUN:1819U21 siRNA stab07 B AAAAAGuGAAAAccuuGAATT B 1649 sense 1935 CAACUCAUGCUAACGCAGCAGUU 1610 31819 JUN:1937U21 siRNA stab07 B AcucAuGcuAAcGcAGcAGTT B 1650 sense 2259 CAUUGACCAAGAACUGCAUGGAC 1611 31820 JUN:2261U21 siRNA stab07 B uuGAccAAGAAcuGcAuGGTT B 1651 sense 2264 ACCAAGAACUGCAUGGACCUAAC 1612 31821 JUN:2266U21 siRNA stab07 B cAAGAAcuGcAuGGAccuATT B 1652 sense 2269 GAACUGCAUGGACCUAACAUUCG 1613 31822 JUN:2271U21 siRNA stab07 B AcuGcAuGGAccuAAcAuuTT B 1653 sense 2270 AACUGCAUGGACCUAACAUUCGA 1614 31823 JUN:2272U21 siRNA stab07 B cuGcAuGGAccuAAcAuucTT B 1654 sense 2272 CUGCAUGGACCUAACAUUCGAUC 1615 31824 JUN:2274U21 siRNA stab07 B GcAuGGAccuAAcAuucGATT B 1655 sense 2274 GCAUGGACCUAACAUUCGAUCUG 1616 31825 JUN:2276U21 siRNA stab07 B AuGGAccuAAcAuucGAucTT B 1656 sense 1817 GGAAAAAGUGAAAACCUUGAAAG 1609 JUN:1837L21 siRNA (1819C) uucAAGGuuuucAcuuuuuTsT 1657 stab11 antisense 1935 CAACUCAUGCUAACGCAGCAGUU 1610 JUN:1955L21 siRNA (1937C) cuGcuGcGuuAGcAuGAGuTsT 1658 stab11 antisense 2259 CAUUGACCAAGAACUGCAUGGAC 1611 JUN:2279L21 siRNA (2261C) ccAucAGuucuuGGucAATsT 1659 stab11 antisense 2264 ACCAAGAACUGCAUGGACCUAAC 1612 JUN:2284L21 siRNA (2266C) uAGGuccAuGcAGuucuuGTsT 1660 stab11 antisense 2269 GAACUGCAUGGACCUAACAUUCG 1613 JUN:2289L21 siRNA (2271C) AAuGuuAGGuccAuGcAGuTsT 1661 stab11 antisense 2270 AACUGCAUGGACCUAACAUUCGA 1614 JUN:2290L21 siRNA (2272C) GAAuGuuAGGuccAuGcAGTsT 1662 stab11 antisense 2272 CUGCAUGGACCUAACAUUCGAUC 1615 JUN:2292L21 siRNA (2274C) ucGAAuGuuAGGuccAuGcTsT 1663 stab11 antisense 2274 GCAUGGACCUAACAUUCGAUCUC 1616 JUN:2294L21 siRNA (2276C) GAucGAAuGuuAGGuccAuTsT 1664 stab11 antisense 1817 GGAAAAAGUGAAAACCUUGAAAG 1609 JUN:1819U21 siRNA stab08 AAAAAGuGAAAAccuuGAATsT 1665 sense 1935 CAACUCAUGCUAACGCAGCAGUU 1610 JUN:1937U21 siRNA stab08 AcucAuGcuAAcGcAGcAGTsT 1666 sense 2259 CAUUGACCAAGAACUGCAUGGAC 1611 JUN:2261U21 siRNA stab08 uuGAccAAGAAcuGcAuGGTsT 1667 sense 2264 ACCAAGAACUGCAUGGACCUAAC 1612 JUN:2266U21 siRNA stab08 cAAGAAcuGcAuGGAccuATsT 1668 sense 2269 GAACUGCAUGGACCUAACAUUCG 1613 JUN:2271U21 siRNA stab08 AcuGcAuGGAccuAAcAuuTsT 1669 sense 2270 AACUGCAUGGACCUAACAUUCGA 1614 JUN:2272U21 siRNA stab08 cuGcAuGGAccuAAcAuucTsT 1670 sense 2272 CUGCAUGGACCUAACAUUCGAUC 1615 JUN:2274U21 siRNA stabo8 GcAuGGAccuAAcAuucGATsT 1671 sense 2274 GCAUGGACCUAACAUUCGAUCUC 1616 JUN:2276U21 siRNA stabo8 AuGGAccuAAcAuucGAucTsT 1672 sense 1817 GGAAAAAGUGAAAACCUUGAAAG 1609 31826 JUN:1837L21 siRNA (1819C) uucAAGGuuuucAcuuuuuTsT 1673 stab08 antisense 1935 CAACUCAUGCUAACGCAGCAGUU 1610 31827 JUN:1955L21 siRNA (1937C) cuGcuGcGuuAGcAuGAGuTsT 1674 stab08 antisense 2259 CAUUGACCAAGAACUGCAUGGAC 1611 31828 JUN:2279L21 siRNA (2261C) ccAuGcAGuucuuGGucAATsT 1675 stab08 antisense 2264 ACCAAGAACUGCAUGGACCUAAC 1612 31829 JUN:2284L21 siRNA (2266C) uAGGuccAuGcAGuucuuGTsT 1676 stab08 antisense 2269 GAACUGCAUGGACCUAACAUUCG 1613 31830 JUN:2289L21 siRNA (2271C) AAuGuuAGGuccAuGcAGuTsT 1677 stab08 antisense 2270 AACUGCAUGGACCUAACAUUCGA 1614 31831 JUN:2290L21 siRNA (2272C) GAAuGuuAGGuccAuGcAGTsT 1678 stab08 antisense 2272 CUGCAUGGACCUAACAUUCGAUC 1615 31832 JUN:2292L21 siRNA (2274C) ucGAAuGuuAGGuccAuGcTsT 1679 stab08 antisense 2274 GCAUGGACCUAACAUUCGAUCUC 1616 31833 JUN:2294L21 siRNA (2276C) GAucGAAuGuuAGGuccAuTsT 1680 stab08 antisense 1817 GGAAAAAGUGAAAACCUUGAAAG 1609 31834 JUN:1819U21 siRNA inv stab07 B AAGuuccAAAAGuGAAAAATT B 1681 sense 1935 CAACUCAUGCUAACGCAGCAGUU 1610 31835 JUN:1937U21 siRNA inv stab07 B GAcGAcGcAAucGuAcucATT B 1682 sense 2259 CAUUGACCAAGAACUGCAUGGAC 1611 31836 JUN:2261U21 siRNA inv stab07 B GGuAcG uc AAGAAccAGuuTT B 1683 sense 2264 ACCAAGAACUGCAUGGACCUAAC 1612 31837 JUN:2266U21 siRNA inv stab07 B AuccAGGuAcGucAAGAAcTT B 1684 sense 2269 GAACUGCAUGGACCUAACAUUCG 1613 31838 JUN:2271U21 siRNA inv stab07 B uuAcAAuccAGGuAcGucATT B 1685 sense 2270 AACUGCAUGGACCUAACAUUCGA 1614 31839 JUN:2272U21 siRNA inv stab07 B cuuAcAAuccAGGuAcGucTT B 1686 sense 2272 CUGCAUGGACCUAACAUUCGAUC 1615 31840 JUN:2274U21 siRNA inv stab07 B AGcuuAcAAuccAGGuAcGTT B 1687 sense 2274 GCAUGGACCUAACAUUCGAUCUC 1616 31841 JUN:2276U21 siRNA inv stab07 B cuAGcuuAcAAuccAGGuATT B 1688 sense 1817 GGAAAAAGUGAAAACCUUGAAAG 1609 31842 JUN:1837L21 siRNA (1819C) uuuuucAcuuuuGGAAcuuTsT 1689 inv stab08 antisense 1935 CAACUCAUGCUAACGCAGCAGUU 1610 31843 JUN:1955L21 siRNA (1937C) uGAGuAcGAuuGcGucGucTsT 1690 inv stab08 antisense 2259 CAUUGACCAAGAACUGCAUGGAC 1611 31844 JUN:2279L21 siRNA (2261C) AAcuGGuucuuGAcGuAccTsT 1691 inv stab08 antisense 2264 ACCAAGAACUGCAUGGACCUAAC 1612 31845 JUN:2284L21 siRNA (2266C) GuucuuGAcGuAccuGGAuTsT 1692 inv stab08 antisense 2269 GAACUGCAUGGACCUAACAUUCG 1613 31846 JUN:2289L21 siRNA (2271C) uGAcGuAccuGGAuuGuAATsT 1693 inv stab08 antisense 2270 AACUGCAUGGACCUAACAUUCGA 1614 31847 JUN:2290L21 siRNA (2272C) GAcGuAccuGGAuuGuAAGTsT 1694 inv stab08 antisense 2272 CUGCAUGGACCUAACAUUCGAUC 1615 31848 JUN:2292L21 siRNA (2274C) cGuAccuGGAuuGuAAGcuTsT 1695 inv stab08 antisense 2274 GCAUGGACCUAACAUUCGAUCUC 1616 31849 JUN:2294L21 siRNA (2276C) uAccuGGAuuGuAAGcuAGTsT 1696 inv stab08 antisense Uppercase = ribonucleotide u,c = 2′-deoxy-2′-fluoro U, C A = 2′-O-methyl Adenosine G = 2′-O-methyl Guanosine T = thymidine B = inverted deoxy abasic s = phosphorothioate linkage A = deoxy Adenosine G = deoxy Guanosine

TABLE IV Non-limiting examples of Stabilization Chemistries for chemically modified siNA constructs Chemistry pyrimidine Purine cap p = S Strand “Stab 1” Ribo Ribo — 5 at 5′-end S/AS 1 at 3′-end “Stab 2” Ribo Ribo — All linkages Usually AS “Stab 3” 2′-fluoro Ribo — 4 at 5′-end Usually S 4 at 3′-end “Stab 4” 2′-fluoro Ribo 5′ and 3′-ends — Usually S “Stab 5” 2′-fluoro Ribo — 1 at 3′-end Usually AS “Stab 6” 2′-O-Methyl Ribo 5′ and 3′-ends — Usually S “Stab 7” 2′-fluoro 2′-deoxy 5′ and 3′-ends — Usually S “Stab 8” 2′-fluoro 2′-O-Methyl — 1 at 3′-end S or AS “Stab 9” Ribo Ribo 5′ and 3′-ends — Usually S “Stab 10” Ribo Ribo — 1 at 3′-end Usually AS “Stab 11” 2′-fluoro 2′-deoxy — 1 at 3′-end Usually AS Stab 12 2′-fluoro LNA 5′ and 3′-ends Usually S “Stab 13” 2′-fluoro LNA 1 at 3′-end Usually AS “Stab 14” 2′-fluoro 2′-deoxy 2 at 5′-end Usually AS 1 at 3′-end “Stab 15” 2′-deoxy 2′-deoxy 2 at 5′-end Usually AS 1 at 3′-end “Stab 16 Ribo 2′-O-Methyl 5′ and 3′-ends Usually S “Stab 17” 2′-O-Methyl 2′-O-Methyl 5′ and 3′-ends Usually S “Stab 18” 2′-fluoro 2′-O-Methyl 1 at 3′-end Usually AS CAP = any terminal cap, see for example FIG. 10. All Stab 1-18 chemistries can comprise 3′-terminal thymidine (TT) residues All Stab 1-18 chemistries typically comprise 21 nucleotides, but can vary as described herein. S = sense strand AS = antisense strand

TABLE V A. 2.5 μmol Synthesis Cycle ABI 394 Instrument Reagent Equivalents Amount Wait Time* DNA Wait Time* 2′-O-methyl Wait Time*RNA Phosphoramidites 6.5 163 μL 45 sec 2.5 min 7.5 min S-Ethyl Tetrazole 23.8 238 μL 45 sec 2.5 min 7.5 min Acetic Anhydride 100 233 μL 5 sec 5 sec 5 sec N-Methyl 186 233 μL 5 sec 5 sec 5 sec Imidazole TCA 176 2.3 mL 21 sec 21 sec 21 sec Iodine 11.2 1.7 mL 45 sec 45 sec 45 sec Beaucage 12.9 645 μL 100 sec 300 sec 300 sec Acetonitrile NA 6.67 mL NA NA NA B. 0.2 μmol Synthesis Cycle ABI 394 Instrument Reagent Equivalents Amount Wait Time* DNA Wait Time* 2′-O-methyl Wait Time*RNA Phosphoramidites 15 31 μL 45 sec 233 sec 465 sec S-Ethyl Tetrazole 38.7 31 μL 45 sec 233 min 465 sec Acetic Anhydride 655 124 μL 5 sec 5 sec 5 sec N-Methyl 1245 124 μL 5 sec 5 sec 5 sec Imidazole TCA 700 732 μL 10 sec 10 sec 10 sec Iodine 20.6 244 μL 15 sec 15 sec 15 sec Beaucage 7.7 232 μL 100 sec 300 sec 300 sec Acetonitrile NA 2.64 mL NA NA NA C. 0.2 μmol Synthesis Cycle 96 well Instrument Equivalents: DNA/ Amount: DNA/2′-O- Wait Time* 2′-O- Reagent 2′-O-methyl/Ribo methyl/Ribo Wait Time* DNA methyl Wait Time* Ribo Phosphoramidites 22/33/66 40/60/120 μL 60 sec 180 sec 360 sec S-Ethyl Tetrazole  70/105/210 40/60/120 μL 60 sec 180 min 360 sec Acetic Anhydride 265/265/265 50/50/50 μL 10 sec 10 sec 10 sec N-Methyl 502/502/502 50/50/50 μL 10 sec 10 sec 10 sec Imidazole TCA 238/475/475 250/500/500 μL 15 sec 15 sec 15 sec Iodine 6.8/6.8/6.8 80/80/80 μL 30 sec 30 sec 30 sec Beaucage 34/51/51 80/120/120 100 sec 200 sec 200 sec Acetonitrile NA 1150/1150/1150 μL NA NA NA Wait time does not include contact time during delivery. Tandem synthesis utilizes double coupling of linker molecule 

1. A chemically modified nucleic acid molecule, wherein: (a) the nucleic acid molecule comprises a sense strand and a separate antisense strand, each strand having one or more pyrimidine nucleotides and one or more purine nucleotides; (b) each strand of the nucleic acid molecule is independently 18 to 27 nucleotides in length; (c) an 18 to 27 nucleotide sequence of the antisense strand is complementary to a human c-Jun RNA sequence comprising SEQ ID NO:1715; (d) an 18 to 27 nucleotide sequence of the sense strand is complementary to the antisense strand and comprises an 18 to 27 nucleotide sequence of the human RNA sequence; and (e) 50 percent or more of the nucleotides in at least one strand comprise a 2′-sugar modification, wherein the 2′-sugar modification of any of the pyrimidine nucleotides differs from the 2′-sugar modification of any of the purine nucleotides.
 2. The nucleic acid molecule of claim 1, wherein 50 percent or more of the nucleotides in each strand comprise a 2′-sugar modification.
 3. The nucleic acid molecule of claim 1, wherein the 2′-sugar modification is selected from the group consisting of 2′-deoxy-2′-fluoro, 2′-O-methyl, and 2′-deoxy.
 4. The nucleic acid of claim 3, wherein the 2′-deoxy-2′-fluoro sugar modification is a pyrimidine modification.
 5. The nucleic acid of claim 3, wherein the 2′-deoxy sugar modification is a pyrimidine modification.
 6. The nucleic acid of claim 3, wherein the 2′-O-methyl sugar modification is a pyrimidine modification.
 7. The nucleic acid molecule of claim 4, wherein said pyrimidine modification is in the sense strand, the antisense strand, or both the sense strand and antisense strand.
 8. The nucleic acid molecule of claim 6, wherein said pyrimidine modification is in the sense strand, the antisense strand, or both the sense strand and antisense strand.
 9. The nucleic acid molecule of claim 3, wherein the 2′-deoxy sugar modification is a purine modification.
 10. The nucleic acid molecule of claim 3, wherein the 2′-O-methyl sugar modification is a purine modification.
 11. The nucleic acid molecule of claim 9, wherein the purine modification is in the sense strand.
 12. The nucleic acid molecule of claim 10, wherein the purine modification is in the antisense strand.
 13. The nucleic acid molecule of claim 1, wherein the nucleic acid molecule comprises ribonucleotides.
 14. The nucleic acid molecule of claim 1, wherein the sense strand includes a terminal cap moiety at the 5′-end, the 3′-end, or both of the 5′- and 3′-ends.
 15. The nucleic acid molecule of claim 14, wherein the terminal cap moiety is an inverted deoxy abasic moiety.
 16. The nucleic acid molecule of claim 1, wherein said nucleic acid molecule includes one or more phosphorothioate internucleotide linkages.
 17. The nucleic acid molecule of claim 16, wherein one of the phosphorothioate internucleotide linkages is at the 3′-end of the antisense strand.
 18. The nucleic acid molecule of claim 1, wherein the 5′-end of the antisense strand includes a terminal phosphate group.
 19. The nucleic acid molecule of claim 1, wherein the sense strand, the antisense strand, or both the sense strand and the antisense strand include a 3′-overhang.
 20. A composition comprising the nucleic acid molecule of claim 1, in a pharmaceutically acceptable carrier or diluent. 